Clazz.declarePackage ("JS");
Clazz.load (["JS.ScriptExt"], "JS.CmdExt", ["java.lang.Boolean", "$.Float", "$.Long", "java.util.Hashtable", "$.Map", "JU.AU", "$.BS", "$.Base64", "$.Lst", "$.M3", "$.M4", "$.Measure", "$.P3", "$.P4", "$.PT", "$.Quat", "$.SB", "$.V3", "J.api.Interface", "J.atomdata.RadiusData", "J.c.STER", "$.VDW", "J.i18n.GT", "JM.Atom", "$.AtomCollection", "$.BondSet", "$.LabelToken", "JS.SV", "$.ScriptCompiler", "$.ScriptError", "$.ScriptEval", "$.ScriptInterruption", "$.ScriptMathProcessor", "$.ScriptParam", "$.T", "JU.BSUtil", "$.BoxInfo", "$.C", "$.Edge", "$.Elements", "$.Escape", "$.Logger", "$.Parser", "$.Point3fi", "$.SimpleUnitCell", "JV.FileManager", "$.JC", "$.StateManager", "$.Viewer"], function () {
c$ = Clazz.declareType (JS, "CmdExt", JS.ScriptExt);
Clazz.makeConstructor (c$, 
function () {
Clazz.superConstructor (this, JS.CmdExt, []);
});
Clazz.overrideMethod (c$, "dispatch", 
function (iTok, b, st) {
this.chk = this.e.chk;
this.slen = this.e.slen;
this.st = st;
switch (iTok) {
case 1073741866:
st[0].value = this.prepareBinaryOutput (st[0]);
return null;
case 4098:
this.assign ();
break;
case 134221829:
this.cache ();
break;
case 4102:
this.calculate ();
break;
case 4103:
this.capture ();
break;
case 4105:
this.centerAt ();
break;
case 134221831:
this.compare ();
break;
case 528395:
this.console ();
break;
case 4106:
this.connect (1);
break;
case 1094717448:
this.configuration ();
break;
case 134221834:
this.data ();
break;
case 1613238294:
this.connect (0);
break;
case 4120:
this.image ();
break;
case 4122:
this.invertSelected ();
break;
case 4124:
this.macro ();
break;
case 4125:
this.mapProperty ();
break;
case 4126:
this.minimize ();
break;
case 1275072532:
this.modulation ();
break;
case 4130:
this.mutate ();
break;
case 4131:
this.navigate ();
break;
case 4133:
case 134221850:
case 4138:
this.plot (st);
break;
case 134222350:
this.show ();
break;
case 528443:
this.stereo ();
break;
case 1814695966:
this.unitcell (b ? 2 : 1);
break;
case 134221856:
return this.write (b ? st : null);
case 6:
this.measure ();
break;
case 21:
this.polyhedra ();
break;
case 20:
this.ellipsoid ();
break;
case 4:
this.struts ();
break;
}
return null;
}, "~N,~B,~A");
Clazz.defineMethod (c$, "macro", 
 function () {
var key = this.e.optParameterAsString (1);
if (key.length == 0) return;
if (this.chk) return;
var macro = JV.JC.getMacro (key);
if (macro == null) {
this.showString ("macro " + key + " could not be found. Current macros include:\n" + JV.JC.getMacroList ());
return;
}this.showString ("running " + macro);
this.e.cmdScript (4124, macro, null);
});
Clazz.defineMethod (c$, "evalParallel", 
function (context, shapeManager) {
this.chk = this.e.chk;
this.slen = this.e.slen;
var se =  new JS.ScriptEval ().setViewer (this.vwr);
se.historyDisabled = true;
se.compiler =  new JS.ScriptCompiler (this.vwr);
se.sm = shapeManager;
try {
se.restoreScriptContext (context, true, false, false);
se.allowJSThreads = false;
se.dispatchCommands (false, false, false);
} catch (ex) {
if (Clazz.exceptionOf (ex, Exception)) {
this.e.vwr.setStringProperty ("_errormessage", "" + ex);
if (se.thisContext == null) {
JU.Logger.error ("Error evaluating context " + ex);
ex.printStackTrace ();
}return false;
} else {
throw ex;
}
}
return true;
}, "JS.ScriptContext,JV.ShapeManager");
Clazz.defineMethod (c$, "getBitsetIdent", 
function (bs, label, tokenValue, useAtomMap, index, isExplicitlyAll) {
var isAtoms = !(Clazz.instanceOf (tokenValue, JM.BondSet));
if (isAtoms) {
if (label == null) label = this.vwr.getStandardLabelFormat (0);
 else if (label.length == 0) label = "%[label]";
}var pt = (label == null ? -1 : label.indexOf ("%"));
var haveIndex = (index != 2147483647);
if (bs == null || this.chk || isAtoms && pt < 0) {
if (label == null) label = "";
return isExplicitlyAll ?  Clazz.newArray (-1, [label]) : label;
}var modelSet = this.vwr.ms;
var n = 0;
var labeler = modelSet.getLabeler ();
var indices = (isAtoms || !useAtomMap ? null : (tokenValue).associatedAtoms);
if (indices == null && label != null && label.indexOf ("%D") > 0) indices = this.vwr.ms.getAtomIndices (bs);
var asIdentity = (label == null || label.length == 0);
var htValues = (isAtoms || asIdentity ? null : JM.LabelToken.getBondLabelValues ());
var tokens = (asIdentity ? null : isAtoms ? labeler.compile (this.vwr, label, '\0', null) : labeler.compile (this.vwr, label, '\1', htValues));
var nmax = (haveIndex ? 1 : bs.cardinality ());
var sout =  new Array (nmax);
var ptTemp =  new JU.P3 ();
for (var j = (haveIndex ? index : bs.nextSetBit (0)); j >= 0; j = bs.nextSetBit (j + 1)) {
var str;
if (isAtoms) {
if (asIdentity) str = modelSet.at[j].getInfo ();
 else str = labeler.formatLabelAtomArray (this.vwr, modelSet.at[j], tokens, '\0', indices, ptTemp);
} else {
var bond = modelSet.bo[j];
if (asIdentity) str = bond.getIdentity ();
 else str = labeler.formatLabelBond (this.vwr, bond, tokens, htValues, indices, ptTemp);
}str = JU.PT.formatStringI (str, "#", (n + 1));
sout[n++] = str;
if (haveIndex) break;
}
return nmax == 1 && !isExplicitlyAll ? sout[0] : sout;
}, "JU.BS,~S,~O,~B,~N,~B");
Clazz.defineMethod (c$, "getLoadSymmetryParams", 
function (i, sOptions, htParams) {
var eval = this.e;
this.chk = eval.chk;
this.slen = eval.slen;
var lattice = null;
var tok = this.tokAt (i);
if (tok == 1073742332 || tok == 8) {
lattice = eval.getPointOrPlane (i, false, true, false, true, 3, 3, true);
tok = this.tokAt (i = eval.iToken + 1);
}switch (tok) {
case 1073741938:
case 1073742080:
case 1094713350:
case 1073742163:
case 1073742114:
case 1073742152:
case 1814695966:
if (lattice == null) lattice = JU.P3.new3 (555, 555, -1);
eval.iToken = i - 1;
}
var offset = null;
if (lattice != null) {
htParams.put ("lattice", lattice);
i = eval.iToken + 1;
sOptions.append (" " + JU.SimpleUnitCell.escapeMultiplier (lattice));
i = this.checkPacked (i, htParams, sOptions);
if (this.tokAt (i) == 1094713350) {
htParams.put ("centroid", Boolean.TRUE);
sOptions.append (" CENTROID");
i = this.checkPacked (++i, htParams, sOptions);
}if (this.tokAt (i) == 1073742163) {
var supercell;
sOptions.append (" SUPERCELL ");
if (eval.isPoint3f (++i)) {
var pt = this.getPoint3f (i, false);
if (pt.x != Clazz.floatToInt (pt.x) || pt.y != Clazz.floatToInt (pt.y) || pt.z != Clazz.floatToInt (pt.z) || pt.x < 1 || pt.y < 1 || pt.z < 1) {
eval.iToken = i;
this.invArg ();
}supercell = pt;
i = eval.iToken;
} else {
supercell = this.stringParameter (i);
}sOptions.append (JU.Escape.e (supercell));
htParams.put ("supercell", supercell);
i = this.checkPacked (++i, htParams, sOptions);
}var distance = 0;
if (this.tokAt (i) == 1073742114) {
i++;
distance = this.floatParameter (i++);
sOptions.append (" range " + distance);
}htParams.put ("symmetryRange", Float.$valueOf (distance));
var spacegroup = null;
var sg;
var iGroup = -2147483648;
if (this.tokAt (i) == 1073742152) {
++i;
spacegroup = JU.PT.rep (this.paramAsStr (i++), "''", "\"");
sOptions.append (" spacegroup " + JU.PT.esc (spacegroup));
if (spacegroup.equalsIgnoreCase ("ignoreOperators")) {
iGroup = -999;
} else {
if (spacegroup.length == 0) {
sg = this.vwr.getCurrentUnitCell ();
if (sg != null) spacegroup = sg.getSpaceGroupName ();
} else {
if (spacegroup.indexOf (",") >= 0) if ((lattice.x < 9 && lattice.y < 9 && lattice.z == 0)) spacegroup += "#doNormalize=0";
}htParams.put ("spaceGroupName", spacegroup);
iGroup = -2;
}}var fparams = null;
if (this.tokAt (i) == 1814695966) {
++i;
var s = eval.optParameterAsString (i);
if (s.length == 0) {
sg = this.vwr.getCurrentUnitCell ();
if (sg != null) {
fparams = sg.getUnitCellAsArray (true);
offset = sg.getCartesianOffset ();
}} else {
if (this.tokAt (i) == 4) {
fparams =  Clazz.newFloatArray (6, 0);
JU.SimpleUnitCell.setOabc (s, fparams, null);
} else {
fparams = eval.floatParameterSet (i, 6, 9);
}}if (fparams == null || fparams.length != 6 && fparams.length != 9) this.invArg ();
sOptions.append (" unitcell [");
for (var j = 0; j < fparams.length; j++) sOptions.append ((j == 0 ? "" : " ") + fparams[j]);

sOptions.append ("]");
htParams.put ("unitcell", fparams);
if (iGroup == -2147483648) iGroup = -1;
i = eval.iToken + 1;
}if (iGroup != -2147483648) htParams.put ("spaceGroupIndex", Integer.$valueOf (iGroup));
}if (offset != null) eval.coordinatesAreFractional = false;
 else if (this.tokAt (i) == 1073742066) offset = this.getPoint3f (++i, true);
if (offset != null) {
if (eval.coordinatesAreFractional) {
offset.setT (eval.fractionalPoint);
htParams.put ("unitCellOffsetFractional", (eval.coordinatesAreFractional ? Boolean.TRUE : Boolean.FALSE));
sOptions.append (" offset {" + offset.x + " " + offset.y + " " + offset.z + "/1}");
} else {
sOptions.append (" offset " + JU.Escape.eP (offset));
}htParams.put ("unitCellOffset", offset);
i = eval.iToken + 1;
}return i;
}, "~N,JU.SB,java.util.Map");
Clazz.defineMethod (c$, "checkPacked", 
 function (i, htParams, sOptions) {
switch (this.tokAt (i)) {
case 1073741938:
htParams.put ("packed", Boolean.TRUE);
var oabc = null;
var tok = this.tokAt (++i);
switch (tok) {
case 1814695966:
case 1678381065:
break;
default:
if (this.e.isArrayParameter (i)) {
oabc = this.e.getPointArray (i, -1, false);
i = this.e.iToken;
} else if (this.isFloatParameter (i)) {
var d = this.floatParameter (i);
oabc =  Clazz.newArray (-1, [ new JU.P3 (), JU.P3.new3 (d, d, d)]);
} else {
oabc =  new Array (0);
--i;
}}
i++;
if (this.e.chk) return i;
switch (tok) {
case 1814695966:
var type = this.e.optParameterAsString (i++).toLowerCase ();
if (JU.PT.isOneOf (type, ";conventional;primitive;")) {
htParams.put ("fillRange", type);
sOptions.append (" FILL UNITCELL \"" + type + "\"");
return i;
}var unitCell = this.vwr.getCurrentUnitCell ();
if (unitCell != null) {
oabc = JU.BoxInfo.toOABC (unitCell.getUnitCellVerticesNoOffset (), unitCell.getCartesianOffset ());
break;
}case 1678381065:
oabc = JU.BoxInfo.toOABC (this.vwr.ms.getBBoxVertices (), null);
break;
}
switch (oabc.length) {
case 2:
var a = oabc[1];
oabc =  Clazz.newArray (-1, [oabc[0], JU.P3.newP (oabc[0]),  new JU.P3 (),  new JU.P3 ()]);
oabc[1].x = a.x;
oabc[2].y = a.y;
oabc[3].z = a.z;
break;
case 3:
oabc =  Clazz.newArray (-1, [ new JU.P3 (), oabc[0], oabc[1], oabc[2]]);
break;
case 4:
break;
default:
oabc =  Clazz.newArray (-1, [ new JU.P3 (), JU.P3.new3 (10, 0, 0), JU.P3.new3 (0, 10, 0), JU.P3.new3 (0, 0, 10)]);
}
htParams.put ("fillRange", oabc);
sOptions.append (" FILL [" + oabc[0] + oabc[1] + oabc[2] + oabc[3] + "]");
break;
case 1073742080:
var f = NaN;
if (this.isFloatParameter (++i)) f = this.floatParameter (i++);
if (!this.e.chk) {
htParams.put ("packed", Boolean.TRUE);
sOptions.append (" PACKED");
if (!Float.isNaN (f)) {
htParams.put ("packingError", Float.$valueOf (f));
sOptions.append (" " + f);
}}break;
}
return i;
}, "~N,java.util.Map,JU.SB");
Clazz.defineMethod (c$, "cache", 
 function () {
var tok = this.tokAt (1);
var fileName = null;
var n = 2;
switch (tok) {
case 1275069441:
case 1073742119:
fileName = this.e.optParameterAsString (n++);
case 1073741882:
this.checkLength (n);
if (!this.chk) {
if ("all".equals (fileName)) fileName = null;
var nBytes = this.vwr.cacheFileByName (fileName, tok == 1275069441);
this.showString (nBytes < 0 ? "cache cleared" : nBytes + " bytes " + (tok == 1275069441 ? " cached" : " removed"));
}break;
default:
this.invArg ();
}
});
Clazz.defineMethod (c$, "calculate", 
 function () {
var isSurface = false;
var asDSSP = false;
var bs1 = null;
var bs2 = null;
var eval = this.e;
var n = -2147483648;
var version = 2;
if ((eval.iToken = eval.slen) >= 2) {
eval.clearDefinedVariableAtomSets ();
switch (this.getToken (1).tok) {
case 1073741824:
this.checkLength (2);
break;
case 1086324752:
eval.iToken = 1;
bs1 = (this.slen == 2 ? null : this.atomExpressionAt (2));
eval.checkLast (eval.iToken);
if (!this.chk) eval.showString (this.vwr.calculateChirality (bs1));
return;
case 1631586315:
this.checkLength (2);
if (this.chk) return;
n = this.vwr.calculateFormalCharges (null);
this.showString (J.i18n.GT.i (J.i18n.GT.$ ("{0} charges modified"), n));
return;
case 1075838996:
this.checkLength (2);
if (!this.chk) this.vwr.ms.assignAromaticBondsBs (true, null);
return;
case 1613238294:
if (eval.slen != 2) {
asDSSP = (this.tokAt (++eval.iToken) == 1639976963);
if (asDSSP) bs1 = this.vwr.bsA ();
 else bs1 = this.atomExpressionAt (eval.iToken);
if (!asDSSP && !(asDSSP = (this.tokAt (++eval.iToken) == 1639976963))) bs2 = this.atomExpressionAt (eval.iToken);
}if (this.chk) return;
n = this.vwr.autoHbond (bs1, bs2, false);
if (n != -2147483648) eval.report (J.i18n.GT.i (J.i18n.GT.$ ("{0} hydrogen bonds"), Math.abs (n)), false);
return;
case 1612709900:
var andBond = (this.tokAt (2) == 1073742335);
if (andBond) eval.iToken++;
bs1 = (this.slen == (andBond ? 3 : 2) ? null : this.atomExpressionAt (andBond ? 3 : 2));
eval.checkLast (eval.iToken);
if (!this.chk) {
this.vwr.addHydrogens (bs1, false, false);
if (andBond) {
if (bs1 == null) bs1 = this.vwr.bsA ();
this.vwr.makeConnections (0.1, 1e8, 515, 1073742025, bs1, bs1, null, false, false, 0);
this.vwr.ms.assignAromaticBondsBs (true, null);
}}return;
case 1111492619:
eval.iToken = 1;
bs1 = (this.slen == 2 ? null : this.atomExpressionAt (2));
eval.checkLast (eval.iToken);
if (!this.chk) eval.getPartialCharges (bs1);
return;
case 1088421903:
case 134217762:
if (!this.chk) {
if (this.tokAt (2) == 1275203608) {
var id = (this.tokAt (3) == 4 ? this.stringParameter (3) : null);
bs1 = (id != null || this.slen == 3 ? null : this.atomExpressionAt (3));
var data =  Clazz.newArray (-1, [id, null, bs1]);
this.showString (eval.getShapePropertyData (21, "symmetry", data) ? data[1] : "");
} else {
this.showString (this.vwr.ms.calculatePointGroup (this.vwr.bsA ()));
}}return;
case 1111490574:
this.checkLength (2);
if (!this.chk) {
this.vwr.calculateStraightness ();
this.vwr.addStateScript ("set quaternionFrame '" + this.vwr.getQuaternionFrame () + "'; calculate straightness", false, true);
}return;
case 1639976963:
bs1 = (this.slen < 4 || this.isFloatParameter (3) ? null : this.atomExpressionAt (2));
switch (this.tokAt (++eval.iToken)) {
case 4138:
break;
case 1111490587:
if (this.chk) return;
eval.showString (this.vwr.getAnnotationParser (true).calculateDSSRStructure (this.vwr, bs1));
return;
case 1073741915:
asDSSP = true;
version = (this.slen == eval.iToken + 1 ? 2 : Clazz.floatToInt (this.floatParameter (++eval.iToken)));
break;
case 0:
asDSSP = this.vwr.getBoolean (603979826);
break;
default:
this.invArg ();
}
if (!this.chk) this.showString (this.vwr.calculateStructures (bs1, asDSSP, true, version));
return;
case 659482:
bs1 = (eval.iToken + 1 < this.slen ? this.atomExpressionAt (++eval.iToken) : null);
bs2 = (eval.iToken + 1 < this.slen ? this.atomExpressionAt (++eval.iToken) : null);
this.checkLength (++eval.iToken);
if (!this.chk) {
n = this.vwr.calculateStruts (bs1, bs2);
if (n > 0) {
this.setShapeProperty (1, "type", Integer.$valueOf (32768));
eval.setShapePropertyBs (1, "color", Integer.$valueOf (0x0FFFFFF), null);
eval.setShapeTranslucency (1, "", "translucent", 0.5, null);
this.setShapeProperty (1, "type", Integer.$valueOf (1023));
}this.showString (J.i18n.GT.i (J.i18n.GT.$ ("{0} struts added"), n));
}return;
case 2097180:
isSurface = true;
case 1111490575:
var isFrom = false;
switch (this.tokAt (2)) {
case 134217759:
eval.iToken++;
break;
case 0:
isFrom = !isSurface;
break;
case 1073741952:
isFrom = true;
eval.iToken++;
break;
default:
isFrom = true;
}
bs1 = (eval.iToken + 1 < this.slen ? this.atomExpressionAt (++eval.iToken) : this.vwr.bsA ());
this.checkLength (++eval.iToken);
if (!this.chk) this.vwr.calculateSurface (bs1, (isFrom ? 3.4028235E38 : -1));
return;
}
}eval.errorStr2 (53, "CALCULATE", "aromatic? hbonds? hydrogen? formalCharge? partialCharge? pointgroup? straightness? structure? struts? surfaceDistance FROM? surfaceDistance WITHIN?");
});
Clazz.defineMethod (c$, "capture", 
 function () {
if (!this.chk && !this.vwr.allowCapture ()) {
this.showString ("Cannot capture on this platform");
return;
}var params = this.vwr.captureParams;
var type = (params == null ? "GIF" : params.get ("type"));
var endTime = 0;
var mode = 0;
var slen = this.e.slen;
var fileName = "";
var looping = (this.vwr.am.animationReplayMode != 1073742070);
var i = 1;
var tok = this.tokAt (i);
var isTransparent = (tok == 603979967);
if (isTransparent) tok = this.tokAt (++i);
switch (tok == 0 ? (tok = 102409) : tok) {
case 4:
fileName = this.e.optParameterAsString (i++);
if (fileName.length == 0) {
mode = 102409;
break;
}var lc = fileName.toLowerCase ();
if (lc.endsWith (".gift") || lc.endsWith (".pngt")) {
isTransparent = true;
fileName = fileName.substring (0, fileName.length - 1);
lc = fileName.toLowerCase ();
} else if (!lc.endsWith (".gif") && !lc.contains (".png")) {
fileName += ".gif";
}if (lc.endsWith (".png")) {
if (!lc.endsWith ("0.png")) fileName = fileName.substring (0, fileName.length - 4) + "0000.png";
type = "PNG";
} else {
type = "GIF";
}if (isTransparent) type += "T";
var pt = fileName.indexOf ("0000.");
var streaming = (pt < 0 || pt != fileName.lastIndexOf (".") - 4);
var isRock = false;
if (this.tokAt (i) == 528411) {
looping = true;
tok = this.tokAt (++i);
}switch (this.tokAt (i)) {
case 1073742129:
isRock = true;
case 1611141175:
var s = null;
var axis = "y";
looping = true;
i++;
if (isRock) {
if (i < slen && this.tokAt (i) != 2) axis = this.e.optParameterAsString (i++).toLowerCase ();
s = "rotate Y 10 10;rotate Y -10 -10;rotate Y -10 -10;rotate Y 10 10";
var n = (i < slen ? this.intParameter (i++) : 5);
if (n < 0) {
s = JU.PT.rep (s, "10;", "" + (-n) + ";");
} else {
s = JU.PT.rep (s, "10", "" + n);
}} else {
if (i < slen) axis = this.e.optParameterAsString (i++).toLowerCase ();
s = "rotate Y 360 30;";
}if (this.chk) return;
this.vwr.setNavigationMode (false);
if (axis === "" || "xyz".indexOf (axis) < 0) axis = "y";
var wf = this.vwr.g.waitForMoveTo;
s = "set waitformoveto true;" + JU.PT.rep (s, "Y", axis) + ";set waitformoveto " + wf;
s = "capture " + (isTransparent ? "transparent " : "") + JU.PT.esc (fileName) + " LOOP;" + s + ";capture end;";
this.e.cmdScript (0, null, s);
return;
case 3:
case 2:
endTime = this.floatParameter (i++);
break;
}
if (this.chk) return;
mode = 1073742031;
params =  new java.util.Hashtable ();
var fps = this.vwr.getInt (553648132);
if (streaming) {
params.put ("streaming", Boolean.TRUE);
if (!looping) this.showString (J.i18n.GT.o (J.i18n.GT.$ ("Note: Enable looping using {0}"),  Clazz.newArray (-1, ["ANIMATION MODE LOOP"])));
this.showString (J.i18n.GT.o (J.i18n.GT.$ ("Animation delay based on: {0}"),  Clazz.newArray (-1, ["ANIMATION FPS " + fps])));
}params.put ("captureFps", Integer.$valueOf (fps));
break;
case 102409:
case 1073741874:
if (params != null) params.put ("captureSilent", Boolean.TRUE);
case 1073742335:
case 1073742334:
this.checkLength (-2);
mode = tok;
break;
default:
this.invArg ();
}
if (this.chk || params == null) return;
params.put ("type", type);
var c = Integer.$valueOf (this.vwr.getBackgroundArgb ());
params.put ("backgroundColor", c);
params.put ("fileName", fileName);
params.put ("quality", Integer.$valueOf (-1));
params.put ("endTime", Long.$valueOf (endTime <= 0 ? -1 : System.currentTimeMillis () + Clazz.floatToLong (endTime * 1000)));
params.put ("captureMode", JS.T.nameOf (mode).toLowerCase ());
params.put ("captureLooping", looping ? Boolean.TRUE : Boolean.FALSE);
var msg = this.vwr.processWriteOrCapture (params);
if (msg == null) msg = "canceled";
JU.Logger.info (msg);
});
Clazz.defineMethod (c$, "centerAt", 
 function () {
var tok = this.getToken (1).tok;
switch (tok) {
case 1073741826:
case 96:
case 1678381065:
break;
default:
this.invArg ();
}
var pt = JU.P3.new3 (0, 0, 0);
if (this.slen == 5) {
pt.x = this.floatParameter (2);
pt.y = this.floatParameter (3);
pt.z = this.floatParameter (4);
} else if (this.e.isCenterParameter (2)) {
pt = this.centerParameter (2);
this.e.checkLast (this.e.iToken);
} else {
this.checkLength (2);
}if (!this.chk && !this.vwr.isJmolDataFrame ()) this.vwr.tm.setCenterAt (tok, pt);
});
Clazz.defineMethod (c$, "compare", 
 function () {
var eval = this.e;
var isQuaternion = false;
var doRotate = false;
var doTranslate = false;
var doAnimate = false;
var isFlexFit = false;
var data1 = null;
var data2 = null;
var bsAtoms1 = null;
var bsAtoms2 = null;
var vAtomSets = null;
var vQuatSets = null;
eval.iToken = 0;
var nSeconds = (this.isFloatParameter (1) ? this.floatParameter (++eval.iToken) : NaN);
var bsFrom = this.atomExpressionAt (++eval.iToken);
var coordTo = null;
var bsTo = null;
if (eval.isArrayParameter (++eval.iToken)) {
coordTo = eval.getPointArray (eval.iToken, -1, false);
} else if (this.tokAt (eval.iToken) != 1140850689) {
bsTo = this.atomExpressionAt (eval.iToken);
}var bsSubset = null;
var isSmiles = false;
var strSmiles = null;
var bs = JU.BSUtil.copy (bsFrom);
if (bsTo != null) bs.or (bsTo);
var isToSubsetOfFrom = (coordTo == null && bsTo != null && bs.equals (bsFrom));
var isFrames = isToSubsetOfFrom;
for (var i = eval.iToken + 1; i < this.slen; ++i) {
switch (this.getToken (i).tok) {
case 4115:
isFrames = true;
break;
case 134218757:
isSmiles = true;
if (this.tokAt (i + 1) != 4) {
strSmiles = "*";
break;
}case 134218756:
strSmiles = this.stringParameter (++i);
break;
case 1677721602:
isFlexFit = true;
doRotate = true;
strSmiles = this.paramAsStr (++i);
if (strSmiles.equalsIgnoreCase ("SMILES")) {
isSmiles = true;
strSmiles = "*";
}break;
case 3:
case 2:
nSeconds = Math.abs (this.floatParameter (i));
if (nSeconds > 0) doAnimate = true;
break;
case 268435504:
break;
case 2109448:
bsSubset = this.atomExpressionAt (++i);
i = eval.iToken;
break;
case 10:
case 1073742325:
if (vQuatSets != null) this.invArg ();
bsAtoms1 = this.atomExpressionAt (eval.iToken);
var tok = (isToSubsetOfFrom ? 0 : this.tokAt (eval.iToken + 1));
bsAtoms2 = (coordTo == null && eval.isArrayParameter (eval.iToken + 1) ? null : (tok == 10 || tok == 1073742325 ? this.atomExpressionAt (++eval.iToken) : JU.BSUtil.copy (bsAtoms1)));
if (bsSubset != null) {
bsAtoms1.and (bsSubset);
if (bsAtoms2 != null) bsAtoms2.and (bsSubset);
}if (bsAtoms2 == null) coordTo = eval.getPointArray (++eval.iToken, -1, false);
 else if (bsTo != null) bsAtoms2.and (bsTo);
if (vAtomSets == null) vAtomSets =  new JU.Lst ();
vAtomSets.addLast ( Clazz.newArray (-1, [bsAtoms1, bsAtoms2]));
i = eval.iToken;
break;
case 7:
if (vAtomSets != null) this.invArg ();
isQuaternion = true;
data1 = eval.getQuaternionArray ((eval.theToken).getList (), 1073742001);
this.getToken (++i);
data2 = eval.getQuaternionArray ((eval.theToken).getList (), 1073742001);
if (vQuatSets == null) vQuatSets =  new JU.Lst ();
vQuatSets.addLast ( Clazz.newArray (-1, [data1, data2]));
break;
case 1073742077:
isQuaternion = true;
break;
case 134217751:
case 1140850689:
isQuaternion = false;
break;
case 528432:
doRotate = true;
break;
case 4160:
doTranslate = true;
break;
default:
this.invArg ();
}
}
if (this.chk) return;
if (isFrames) nSeconds = 0;
if (Float.isNaN (nSeconds) || nSeconds < 0) nSeconds = 1;
 else if (!doRotate && !doTranslate) doRotate = doTranslate = true;
doAnimate = (nSeconds != 0);
var isAtoms = (!isQuaternion && strSmiles == null || coordTo != null);
if (isAtoms) J.api.Interface.getInterface ("JU.Eigen", this.vwr, "script");
if (vAtomSets == null && vQuatSets == null) {
if (bsSubset == null) {
bsAtoms1 = (isAtoms ? this.vwr.getAtomBitSet ("spine") :  new JU.BS ());
if (bsAtoms1.nextSetBit (0) < 0) {
bsAtoms1 = bsFrom;
bsAtoms2 = bsTo;
} else {
bsAtoms2 = JU.BSUtil.copy (bsAtoms1);
bsAtoms1.and (bsFrom);
bsAtoms2.and (bsTo);
}} else {
bsAtoms1 = JU.BSUtil.copy (bsFrom);
bsAtoms2 = JU.BSUtil.copy (bsTo);
bsAtoms1.and (bsSubset);
bsAtoms1.and (bsFrom);
if (bsAtoms2 != null) {
bsAtoms2.and (bsSubset);
bsAtoms2.and (bsTo);
}}vAtomSets =  new JU.Lst ();
vAtomSets.addLast ( Clazz.newArray (-1, [bsAtoms1, bsAtoms2]));
}var bsFrames;
if (isFrames) {
var bsModels = this.vwr.ms.getModelBS (bsFrom, false);
bsFrames =  new Array (bsModels.cardinality ());
for (var i = 0, iModel = bsModels.nextSetBit (0); iModel >= 0; iModel = bsModels.nextSetBit (iModel + 1), i++) bsFrames[i] = this.vwr.getModelUndeletedAtomsBitSet (iModel);

} else {
bsFrames =  Clazz.newArray (-1, [bsFrom]);
}for (var iFrame = 0; iFrame < bsFrames.length; iFrame++) {
bsFrom = bsFrames[iFrame];
var retStddev =  Clazz.newFloatArray (2, 0);
var q = null;
var vQ =  new JU.Lst ();
var centerAndPoints = null;
var vAtomSets2 = (isFrames ?  new JU.Lst () : vAtomSets);
for (var i = 0; i < vAtomSets.size (); ++i) {
var bss = vAtomSets.get (i);
if (isFrames) vAtomSets2.addLast (bss =  Clazz.newArray (-1, [JU.BSUtil.copy (bss[0]), bss[1]]));
bss[0].and (bsFrom);
}
var center = null;
var translation = null;
if (isAtoms) {
if (coordTo != null) {
vAtomSets2.clear ();
vAtomSets2.addLast ( Clazz.newArray (-1, [bsAtoms1, coordTo]));
}try {
centerAndPoints = this.vwr.getCenterAndPoints (vAtomSets2, true);
} catch (ex) {
if (Clazz.exceptionOf (ex, Exception)) {
this.invArg ();
} else {
throw ex;
}
}
var n = centerAndPoints[0].length - 1;
for (var i = 1; i <= n; i++) {
var aij = centerAndPoints[0][i];
var bij = centerAndPoints[1][i];
if (!(Clazz.instanceOf (aij, JM.Atom)) || !(Clazz.instanceOf (bij, JM.Atom))) break;
JU.Logger.info (" atom 1 " + (aij).getInfo () + "\tatom 2 " + (bij).getInfo ());
}
q = JU.Measure.calculateQuaternionRotation (centerAndPoints, retStddev);
var r0 = (Float.isNaN (retStddev[1]) ? NaN : Math.round (retStddev[0] * 100) / 100);
var r1 = (Float.isNaN (retStddev[1]) ? NaN : Math.round (retStddev[1] * 100) / 100);
this.showString ("RMSD " + r0 + " --> " + r1 + " Angstroms");
} else if (isQuaternion) {
if (vQuatSets == null) {
for (var i = 0; i < vAtomSets2.size (); i++) {
var bss = vAtomSets2.get (i);
data1 = this.vwr.getAtomGroupQuaternions (bss[0], 2147483647);
data2 = this.vwr.getAtomGroupQuaternions (bss[1], 2147483647);
for (var j = 0; j < data1.length && j < data2.length; j++) {
vQ.addLast (data2[j].div (data1[j]));
}
}
} else {
for (var j = 0; j < data1.length && j < data2.length; j++) {
vQ.addLast (data2[j].div (data1[j]));
}
}retStddev[0] = 0;
data1 = vQ.toArray ( new Array (vQ.size ()));
q = JU.Quat.sphereMean (data1, retStddev, 0.0001);
this.showString ("RMSD = " + retStddev[0] + " degrees");
} else {
var m4 =  new JU.M4 ();
center =  new JU.P3 ();
if (("*".equals (strSmiles) || "".equals (strSmiles)) && bsFrom != null) try {
strSmiles = this.vwr.getSmiles (bsFrom);
} catch (ex) {
if (Clazz.exceptionOf (ex, Exception)) {
eval.evalError (ex.getMessage (), null);
} else {
throw ex;
}
}
if (isFlexFit) {
var list;
if (bsFrom == null || bsTo == null || (list = eval.getSmilesExt ().getFlexFitList (bsFrom, bsTo, strSmiles, !isSmiles)) == null) return;
this.vwr.setDihedrals (list, null, 1);
}var stddev = eval.getSmilesExt ().getSmilesCorrelation (bsFrom, bsTo, strSmiles, null, null, m4, null, false, null, center, false, 32 | (isSmiles ? 1 : 2));
if (Float.isNaN (stddev)) {
this.showString ("structures do not match");
return;
}if (doTranslate) {
translation =  new JU.V3 ();
m4.getTranslation (translation);
}if (doRotate) {
var m3 =  new JU.M3 ();
m4.getRotationScale (m3);
q = JU.Quat.newM (m3);
}this.showString ("RMSD = " + stddev + " Angstroms");
}if (centerAndPoints != null) center = centerAndPoints[0][0];
if (center == null) {
centerAndPoints = this.vwr.getCenterAndPoints (vAtomSets2, true);
center = centerAndPoints[0][0];
}var pt1 =  new JU.P3 ();
var endDegrees = NaN;
if (doTranslate) {
if (translation == null) translation = JU.V3.newVsub (centerAndPoints[1][0], center);
endDegrees = 1e10;
}if (doRotate) {
if (q == null) eval.evalError ("option not implemented", null);
pt1.add2 (center, q.getNormal ());
endDegrees = q.getTheta ();
if (endDegrees == 0 && doTranslate) {
if (translation.length () > 0.01) endDegrees = 1e10;
 else doRotate = doTranslate = doAnimate = false;
}}if (Float.isNaN (endDegrees) || Float.isNaN (pt1.x)) continue;
var ptsB = null;
if (doRotate && doTranslate && nSeconds != 0) {
var ptsA = this.vwr.ms.getAtomPointVector (bsFrom);
var m4 = JS.ScriptMathProcessor.getMatrix4f (q.getMatrix (), translation);
ptsB = JU.Measure.transformPoints (ptsA, m4, center);
}if (!eval.useThreads ()) doAnimate = false;
if (this.vwr.rotateAboutPointsInternal (eval, center, pt1, endDegrees / nSeconds, endDegrees, doAnimate, bsFrom, translation, ptsB, null, null) && doAnimate && eval.isJS) throw  new JS.ScriptInterruption (eval, "compare", 1);
}
});
Clazz.defineMethod (c$, "configuration", 
 function () {
var bsAtoms = null;
var bsSelected = this.vwr.bsA ();
if (this.slen == 1) {
if (this.chk) return;
bsAtoms = this.vwr.ms.setConformation (bsSelected);
this.vwr.ms.addStateScript ("select", null, bsSelected, null, "configuration", true, false);
} else {
var n;
if (this.isFloatParameter (1)) {
n = this.intParameter (this.e.checkLast (1));
if (this.chk) return;
bsAtoms = this.vwr.ms.getConformation (this.vwr.am.cmi, n - 1, true, null);
this.vwr.addStateScript ("configuration " + n + ";", true, false);
} else {
bsAtoms = this.atomExpressionAt (1);
if (this.chk) return;
n = this.intParameter (this.e.checkLast (this.e.iToken + 1));
this.vwr.addStateScript ("configuration " + JU.Escape.eBS (bsAtoms) + " " + n + ";", true, false);
bsAtoms = this.vwr.ms.getConformation (this.vwr.am.cmi, n - 1, true, bsAtoms);
}}this.setShapeProperty (1, "type", Integer.$valueOf (30720));
this.e.setShapeSizeBs (1, 0, bsAtoms);
this.vwr.autoHbond (bsAtoms, bsAtoms, true);
this.vwr.select (bsAtoms, false, 0, this.e.tQuiet);
});
Clazz.defineMethod (c$, "measure", 
 function () {
var eval = this.e;
var id = null;
var pt = 1;
var colix = 0;
var offset = null;
if (this.slen == 2) switch (this.tokAt (1)) {
case 1073742334:
this.setShapeProperty (6, "hideAll", Boolean.TRUE);
return;
case 12291:
if (!this.chk) this.vwr.clearAllMeasurements ();
return;
}
this.vwr.shm.loadShape (6);
switch (this.tokAt (1)) {
case 134218756:
var smarts = this.stringParameter (this.slen == 3 ? 2 : 4);
if (this.chk) return;
var atoms = this.vwr.ms.at;
var ac = this.vwr.ms.ac;
var maps = null;
try {
maps = this.vwr.getSmilesMatcher ().getCorrelationMaps (smarts, atoms, ac, this.vwr.bsA (), 2);
} catch (ex) {
if (Clazz.exceptionOf (ex, Exception)) {
eval.evalError (ex.getMessage (), null);
} else {
throw ex;
}
}
if (maps == null) return;
this.setShapeProperty (6, "maps", maps);
return;
}
switch (this.slen) {
case 2:
switch (this.getToken (pt).tok) {
case 0:
case 1073742335:
this.vwr.shm.loadShape (6);
this.setShapeProperty (6, "hideAll", Boolean.FALSE);
return;
case 1073742001:
if (!this.chk) eval.showStringPrint (this.vwr.getMeasurementInfoAsString (), false);
return;
case 4:
this.setShapeProperty (6, "setFormats", this.stringParameter (1));
return;
}
eval.errorStr (24, "ON, OFF, DELETE");
break;
case 3:
switch (this.getToken (1).tok) {
case 12291:
if (this.getToken (2).tok == 1073742327) {
if (!this.chk) this.vwr.clearAllMeasurements ();
} else {
var i = this.intParameter (2) - 1;
if (!this.chk) this.vwr.deleteMeasurement (i);
}return;
}
}
var nAtoms = 0;
var expressionCount = 0;
var modelIndex = -1;
var atomIndex = -1;
var ptFloat = -1;
var countPlusIndexes =  Clazz.newIntArray (5, 0);
var rangeMinMax =  Clazz.newFloatArray (-1, [3.4028235E38, 3.4028235E38]);
var isAll = false;
var isAllConnected = false;
var isNotConnected = false;
var isRange = true;
var rd = null;
var intramolecular = null;
var tokAction = 268435538;
var strFormat = null;
var font = null;
var points =  new JU.Lst ();
var bs =  new JU.BS ();
var value = null;
var tickInfo = null;
var nBitSets = 0;
var mad = 0;
var alignment = null;
for (var i = 1; i < this.slen; ++i) {
switch (this.getToken (i).tok) {
case 1073741974:
if (i != 1) this.invArg ();
id = eval.optParameterAsString (++i);
continue;
case 1073741824:
eval.errorStr (24, "ALL, ALLCONNECTED, DELETE");
break;
default:
this.error (15);
break;
case 268435568:
if (this.tokAt (i + 1) != 134217736) this.invArg ();
i++;
isNotConnected = true;
break;
case 1073741832:
alignment = this.paramAsStr (++i).toLowerCase ();
break;
case 134217736:
case 1073741834:
case 1073742327:
isAllConnected = (eval.theTok == 1073741834);
atomIndex = -1;
isAll = true;
if (isAllConnected && isNotConnected) this.invArg ();
break;
case 1765808134:
colix = JU.C.getColix (eval.getArgbParam (++i));
i = eval.iToken;
break;
case 1073742066:
if (eval.isPoint3f (++i)) {
var p = this.getPoint3f (i, false);
offset =  Clazz.newFloatArray (-1, [1, p.x, p.y, p.z, 0, 0, 0]);
} else {
offset = eval.floatParameterSet (i, 7, 7);
}i = eval.iToken;
break;
case 1665140738:
case 1073741917:
mad = Clazz.floatToInt ((eval.theTok == 1665140738 ? 2000 : 1000) * this.floatParameter (++i));
if (id != null && mad <= 0) mad = -1;
break;
case 3:
if (rd != null) this.invArg ();
isAll = true;
isRange = true;
ptFloat = (ptFloat + 1) % 2;
rangeMinMax[ptFloat] = this.floatParameter (i);
break;
case 12291:
if (tokAction != 268435538) this.invArg ();
tokAction = 12291;
break;
case 4114:
var fontsize = this.floatParameter (++i);
var fontface = this.paramAsStr (++i);
var fontstyle = this.paramAsStr (++i);
if (!this.chk) font = this.vwr.getFont3D (fontface, fontstyle, fontsize);
break;
case 2:
var iParam = this.intParameter (i);
if (isAll) {
isRange = true;
ptFloat = (ptFloat + 1) % 2;
rangeMinMax[ptFloat] = iParam;
} else {
atomIndex = this.vwr.ms.getFirstAtomIndexFromAtomNumber (iParam, this.vwr.getVisibleFramesBitSet ());
if (!this.chk && atomIndex < 0) return;
if (value != null) this.invArg ();
if ((countPlusIndexes[0] = ++nAtoms) > 4) eval.bad ();
countPlusIndexes[nAtoms] = atomIndex;
}break;
case 1094713359:
modelIndex = this.intParameter (++i);
break;
case 1073742334:
if (tokAction != 268435538) this.invArg ();
tokAction = 1073742334;
break;
case 1073742335:
if (tokAction != 268435538) this.invArg ();
tokAction = 1073742335;
break;
case 1073742114:
isAll = true;
isRange = true;
atomIndex = -1;
break;
case 1073741989:
case 1073741990:
intramolecular = Boolean.$valueOf (eval.theTok == 1073741989);
isAll = true;
isNotConnected = (eval.theTok == 1073741990);
break;
case 1648363544:
if (ptFloat >= 0) this.invArg ();
rd = eval.encodeRadiusParameter (i, false, true);
if (rd == null) return;
rd.values = rangeMinMax;
i = eval.iToken;
isNotConnected = true;
isAll = true;
intramolecular = Boolean.$valueOf (false);
if (nBitSets == 1) {
nBitSets++;
nAtoms++;
var bs2 = JU.BSUtil.copy (bs);
JU.BSUtil.invertInPlace (bs2, this.vwr.ms.ac);
bs2.and (this.vwr.ms.getAtomsWithinRadius (5, bs, false, null));
points.addLast (bs2);
}break;
case 12290:
case 10:
case 1073742325:
nBitSets++;
case 1073742332:
case 8:
case 1073742330:
if (atomIndex >= 0) this.invArg ();
var ret =  new Array (1);
value = eval.centerParameter (i, ret);
if (Clazz.instanceOf (ret[0], JU.BS)) {
value = bs = ret[0];
if (!this.chk && bs.length () == 0) return;
}if (Clazz.instanceOf (value, JU.P3)) {
var v =  new JU.Point3fi ();
v.setT (value);
v.mi = modelIndex;
value = v;
}if ((nAtoms = ++expressionCount) > 4) eval.bad ();
i = eval.iToken;
points.addLast (value);
break;
case 4:
strFormat = this.stringParameter (i);
break;
case 1073742164:
tickInfo = eval.tickParamAsStr (i, false, true, true);
i = eval.iToken;
tokAction = 12290;
break;
}
}
if (rd != null && (ptFloat >= 0 || nAtoms != 2) || nAtoms < 2 && id == null && (tickInfo == null || nAtoms == 1)) eval.bad ();
if (strFormat != null && strFormat.indexOf (nAtoms + ":") != 0) strFormat = nAtoms + ":" + strFormat;
if (isRange) {
if (rangeMinMax[1] < rangeMinMax[0]) {
rangeMinMax[1] = rangeMinMax[0];
rangeMinMax[0] = (rangeMinMax[1] == 3.4028235E38 ? 3.4028235E38 : -200);
}}if (this.chk) return;
if (value != null || tickInfo != null) {
if (rd == null) rd =  new J.atomdata.RadiusData (rangeMinMax, 0, null, null);
if (value == null) tickInfo.id = "default";
if (value != null && strFormat != null && tokAction == 268435538) tokAction = 12290;
var text = null;
if (font != null || alignment != null || strFormat != null && strFormat.indexOf ('\n') >= 0) text = (J.api.Interface.getInterface ("JM.Text", this.vwr, "script")).newLabel (this.vwr, font, "", colix, 0, 0, 0);
if (text != null) {
text.pymolOffset = offset;
text.setAlignmentLCR (alignment);
}this.setShapeProperty (6, "measure", this.vwr.newMeasurementData (id, points).set (tokAction, null, rd, strFormat, null, tickInfo, isAllConnected, isNotConnected, intramolecular, isAll, mad, colix, text));
return;
}var propertyValue = (id == null ? countPlusIndexes : id);
switch (tokAction) {
case 12291:
this.setShapeProperty (6, "delete", propertyValue);
break;
case 1073742335:
this.setShapeProperty (6, "show", propertyValue);
break;
case 1073742334:
this.setShapeProperty (6, "hide", propertyValue);
break;
default:
this.setShapeProperty (6, (strFormat == null ? "toggle" : "toggleOn"), propertyValue);
if (strFormat != null) this.setShapeProperty (6, "setFormats", strFormat);
}
});
Clazz.defineMethod (c$, "connect", 
 function (index) {
var eval = this.e;
var distances =  Clazz.newFloatArray (2, 0);
var atomSets =  new Array (2);
atomSets[0] = atomSets[1] = this.vwr.bsA ();
var radius = NaN;
var colorArgb =  Clazz.newIntArray (-1, [-2147483648]);
var distanceCount = 0;
var bondOrder = 131071;
var bo;
var operation = 1073742026;
var isDelete = false;
var haveType = false;
var haveOperation = false;
var translucentLevel = 3.4028235E38;
var isColorOrRadius = false;
var nAtomSets = 0;
var nDistances = 0;
var bsBonds =  new JU.BS ();
var isBonds = false;
var expression2 = 0;
var ptColor = 0;
var energy = 0;
var addGroup = false;
if (this.slen == 1) {
if (!this.chk) this.vwr.rebondState (eval.$isStateScript);
return;
}if (this.tokAt (1) == 1073877011) {
if (!this.chk) this.vwr.connectNBO (this.e.optParameterAsString (2));
return;
}for (var i = index; i < this.slen; ++i) {
switch (this.getToken (i).tok) {
case 1073742335:
case 1073742334:
this.checkLength (2);
if (!this.chk) this.vwr.rebondState (eval.$isStateScript);
return;
case 2:
case 3:
if (nAtomSets > 0) {
if (haveType || isColorOrRadius) eval.error (23);
bo = JU.Edge.getBondOrderFromFloat (this.floatParameter (i));
if (bo == 131071) this.invArg ();
bondOrder = bo;
haveType = true;
break;
}if (++nDistances > 2) eval.bad ();
var dist = this.floatParameter (i);
if (this.tokAt (i + 1) == 268435634) {
dist = -dist / 100;
i++;
}distances[distanceCount++] = dist;
break;
case 12290:
case 10:
case 1073742325:
if (nAtomSets > 2 || isBonds && nAtomSets > 0) eval.bad ();
if (haveType || isColorOrRadius) this.invArg ();
atomSets[nAtomSets++] = this.atomExpressionAt (i);
isBonds = eval.isBondSet;
if (nAtomSets == 2) {
var pt = eval.iToken;
for (var j = i; j < pt; j++) if (this.tokAt (j) == 1073741824 && this.paramAsStr (j).equals ("_1")) {
expression2 = i;
break;
}
eval.iToken = pt;
}i = eval.iToken;
break;
case 1086324742:
addGroup = true;
break;
case 1765808134:
case 603979967:
case 1073742074:
isColorOrRadius = true;
translucentLevel = this.getColorTrans (eval, i, false, colorArgb);
i = eval.iToken;
break;
case 1073742086:
var isAuto = (this.tokAt (2) == 1073741852);
this.checkLength (isAuto ? 3 : 2);
if (this.chk) return;
this.vwr.clearModelDependentObjects ();
this.vwr.ms.deleteAllBonds ();
var bsExclude =  new JU.BS ();
this.vwr.ms.setPdbConectBonding (0, 0, bsExclude);
if (isAuto) {
var isLegacy = eval.$isStateScript && this.vwr.getBoolean (603979873);
this.vwr.ms.autoBondBs4 (null, null, bsExclude, null, this.vwr.getMadBond (), isLegacy);
this.vwr.addStateScript ((isLegacy ? "set legacyAutoBonding TRUE;connect PDB AUTO;set legacyAutoBonding FALSE;" : "connect PDB auto;"), false, true);
return;
}this.vwr.addStateScript ("connect PDB;", false, true);
return;
case 1073741830:
case 1073741852:
case 1073741904:
case 1073742025:
case 1073742026:
haveOperation = true;
if (++i != this.slen) this.invArg ();
operation = eval.theTok;
if (operation == 1073741852 && !(bondOrder == 131071 || bondOrder == 2048 || bondOrder == 515)) this.invArg ();
break;
case 659482:
if (!isColorOrRadius) {
colorArgb[0] = 0xFFFFFF;
translucentLevel = 0.5;
radius = this.vwr.getFloat (570425406);
isColorOrRadius = true;
}if (!haveOperation) {
operation = 1073742026;
haveOperation = true;
}case 1073741824:
if (eval.isColorParam (i)) {
ptColor = -i;
break;
}case 1075838996:
case 1613238294:
var cmd = this.paramAsStr (i);
if ((bo = JS.ScriptParam.getBondOrderFromString (cmd)) == 131071) this.invArg ();
if (haveType) eval.error (18);
haveType = true;
switch (bo) {
case 33:
switch (this.tokAt (i + 1)) {
case 3:
bo = JS.ScriptParam.getPartialBondOrderFromFloatEncodedInt (this.st[++i].intValue);
break;
case 2:
bo = this.intParameter (++i);
break;
}
break;
case 2048:
if (this.tokAt (i + 1) == 2) {
bo = (this.intParameter (++i) << 11);
energy = this.floatParameter (++i);
}break;
case 65537:
if (!haveOperation) {
operation = 1073742025;
haveOperation = true;
}break;
}
bondOrder = bo;
break;
case 1665140738:
radius = this.floatParameter (++i);
isColorOrRadius = true;
break;
case 1073742333:
case 12291:
if (++i != this.slen) this.invArg ();
operation = 12291;
isDelete = true;
isColorOrRadius = false;
break;
default:
ptColor = i;
break;
}
if (i > 0) {
if (ptColor == -i || ptColor == i && eval.isColorParam (i)) {
isColorOrRadius = true;
colorArgb[0] = eval.getArgbParam (i);
i = eval.iToken;
} else if (ptColor == i) {
this.invArg ();
}}}
if (this.chk) return;
if (distanceCount < 2) {
if (distanceCount == 0) distances[0] = 1.0E8;
distances[1] = distances[0];
distances[0] = 0.1;
}if (isColorOrRadius) {
if (!haveType) bondOrder = 65535;
if (!haveOperation) operation = 1073742025;
}var nNew = 0;
var nModified = 0;
var result;
if (expression2 > 0) {
var bs =  new JU.BS ();
this.vwr.definedAtomSets.put ("_1", bs);
var bs0 = atomSets[0];
for (var atom1 = bs0.nextSetBit (0); atom1 >= 0; atom1 = bs0.nextSetBit (atom1 + 1)) {
bs.set (atom1);
result = this.vwr.makeConnections (distances[0], distances[1], bondOrder, operation, bs, this.atomExpressionAt (expression2), bsBonds, isBonds, false, 0);
nNew += Math.abs (result[0]);
nModified += result[1];
bs.clear (atom1);
}
} else {
result = this.vwr.makeConnections (distances[0], distances[1], bondOrder, operation, atomSets[0], atomSets[1], bsBonds, isBonds, addGroup, energy);
nNew += Math.abs (result[0]);
nModified += result[1];
}var report = eval.doReport ();
if (isDelete) {
if (report) eval.report (J.i18n.GT.i (J.i18n.GT.$ ("{0} connections deleted"), nModified), false);
return;
}if (isColorOrRadius) {
this.vwr.selectBonds (bsBonds);
if (!Float.isNaN (radius)) eval.setShapeSizeBs (1, Math.round (radius * 2000), null);
this.finalizeObject (1, colorArgb[0], translucentLevel, 0, false, null, 0, bsBonds);
this.vwr.selectBonds (null);
}if (report) eval.report (J.i18n.GT.o (J.i18n.GT.$ ("{0} new bonds; {1} modified"),  Clazz.newArray (-1, [Integer.$valueOf (nNew), Integer.$valueOf (nModified)])), false);
}, "~N");
Clazz.defineMethod (c$, "console", 
 function () {
switch (this.getToken (1).tok) {
case 1073742334:
if (!this.chk) this.vwr.showConsole (false);
break;
case 1073742335:
if (!this.chk) this.vwr.showConsole (true);
break;
case 1073741882:
if (!this.chk) this.vwr.sm.clearConsole ();
break;
case 134221856:
this.showString (this.stringParameter (2));
break;
default:
this.invArg ();
}
});
Clazz.defineMethod (c$, "data", 
 function () {
var eval = this.e;
var dataString = null;
var dataLabel = null;
var isOneValue = false;
var i;
switch (eval.iToken = this.slen) {
case 5:
dataString = this.paramAsStr (2);
case 4:
case 2:
dataLabel = this.paramAsStr (1);
if (dataLabel.equalsIgnoreCase ("clear")) {
if (!this.chk) this.vwr.setData (null, null, 0, 0, 0, 0, 0);
return;
}if ((i = dataLabel.indexOf ("@")) >= 0) {
dataString = "" + eval.getParameter (dataLabel.substring (i + 1), 4, true);
dataLabel = dataLabel.substring (0, i).trim ();
} else if (dataString == null && (i = dataLabel.indexOf (" ")) >= 0) {
dataString = dataLabel.substring (i + 1).trim ();
dataLabel = dataLabel.substring (0, i).trim ();
isOneValue = true;
}break;
default:
eval.bad ();
}
var dataType = dataLabel.substring (0, (dataLabel + " ").indexOf (" ")).toLowerCase ();
if (dataType.equals ("model") || dataType.equals ("append")) {
eval.cmdLoad ();
return;
}if (this.chk) return;
var isDefault = (dataLabel.toLowerCase ().indexOf ("(default)") >= 0);
if (dataType.equals ("connect_atoms")) {
this.vwr.ms.connect (this.parseDataArray (dataString, false));
return;
}if (dataType.indexOf ("ligand_") == 0) {
this.vwr.setLigandModel (dataLabel.substring (7).toUpperCase () + "_data", dataString.trim ());
return;
}if (dataType.indexOf ("file_") == 0) {
this.vwr.setLigandModel (dataLabel.substring (5) + "_file", dataString.trim ());
return;
}var d =  new Array (4);
if (dataType.equals ("element_vdw")) {
d[0] = dataType;
d[1] = dataString.$replace (';', '\n');
var n = JU.Elements.elementNumberMax;
var eArray =  Clazz.newIntArray (n + 1, 0);
for (var ie = 1; ie <= n; ie++) eArray[ie] = ie;

d[2] = eArray;
d[3] = Integer.$valueOf (0);
this.vwr.setData ("element_vdw", d, n, 0, 0, 0, 0);
return;
}if (dataType.indexOf ("data2d_") == 0) {
d[0] = dataLabel;
d[1] = this.parseDataArray (dataString, false);
d[3] = Integer.$valueOf (2);
this.vwr.setData (dataLabel, d, 0, 0, 0, 0, 0);
return;
}if (dataType.indexOf ("data3d_") == 0) {
d[0] = dataLabel;
d[1] = this.parseDataArray (dataString, true);
d[3] = Integer.$valueOf (3);
this.vwr.setData (dataLabel, d, 0, 0, 0, 0, 0);
return;
}var tokens = JU.PT.getTokens (dataLabel);
if (dataType.indexOf ("property_") == 0 && !(tokens.length == 2 && tokens[1].equals ("set"))) {
var bs = this.vwr.bsA ();
d[0] = dataType;
var atomNumberField = (isOneValue ? 0 : (this.vwr.getP ("propertyAtomNumberField")).intValue ());
var atomNumberFieldColumnCount = (isOneValue ? 0 : (this.vwr.getP ("propertyAtomNumberColumnCount")).intValue ());
var propertyField = (isOneValue ? -2147483648 : (this.vwr.getP ("propertyDataField")).intValue ());
var propertyFieldColumnCount = (isOneValue ? 0 : (this.vwr.getP ("propertyDataColumnCount")).intValue ());
if (!isOneValue && dataLabel.indexOf (" ") >= 0) {
if (tokens.length == 3) {
dataLabel = tokens[0];
atomNumberField = JU.PT.parseInt (tokens[1]);
propertyField = JU.PT.parseInt (tokens[2]);
}if (tokens.length == 5) {
dataLabel = tokens[0];
atomNumberField = JU.PT.parseInt (tokens[1]);
atomNumberFieldColumnCount = JU.PT.parseInt (tokens[2]);
propertyField = JU.PT.parseInt (tokens[3]);
propertyFieldColumnCount = JU.PT.parseInt (tokens[4]);
}}if (atomNumberField < 0) atomNumberField = 0;
if (propertyField < 0) propertyField = 0;
var ac = this.vwr.ms.ac;
var atomMap = null;
var bsTemp = JU.BS.newN (ac);
if (atomNumberField > 0) {
atomMap =  Clazz.newIntArray (ac + 2, 0);
for (var j = 0; j <= ac; j++) atomMap[j] = -1;

for (var j = bs.nextSetBit (0); j >= 0; j = bs.nextSetBit (j + 1)) {
var atomNo = this.vwr.ms.at[j].getAtomNumber ();
if (atomNo > ac + 1 || atomNo < 0 || bsTemp.get (atomNo)) continue;
bsTemp.set (atomNo);
atomMap[atomNo] = j;
}
d[2] = atomMap;
} else {
d[2] = JU.BSUtil.copy (bs);
}d[1] = dataString;
d[3] = Integer.$valueOf (0);
this.vwr.setData (dataType, d, ac, atomNumberField, atomNumberFieldColumnCount, propertyField, propertyFieldColumnCount);
return;
}if ("occupany".equals (dataType)) dataType = "occupancy";
var userType = JM.AtomCollection.getUserSettableType (dataType);
if (userType > -1) {
this.vwr.setAtomData (userType, dataType, dataString, isDefault);
return;
}d[0] = dataLabel;
d[1] = dataString;
d[3] = Integer.$valueOf (0);
this.vwr.setData (dataType, d, 0, 0, 0, 0, 0);
});
Clazz.defineMethod (c$, "ellipsoid", 
 function () {
var eval = this.e;
var mad = 0;
var i = 1;
var translucentLevel = 3.4028235E38;
var checkMore = false;
var isSet = false;
this.setShapeProperty (20, "thisID", null);
switch (this.getToken (1).tok) {
case 1073742335:
mad = 2147483647;
break;
case 1073742334:
break;
case 2:
mad = this.intParameter (1);
break;
case 36867:
this.e.sm.loadShape (20);
this.setShapeProperty (20, "select", this.paramAsStr (2));
i = eval.iToken;
checkMore = true;
isSet = true;
break;
case 1073741974:
case 268435633:
case 1073741824:
this.e.sm.loadShape (20);
if (eval.theTok == 1073741974) i++;
this.setShapeId (20, i, false);
i = eval.iToken;
checkMore = true;
break;
default:
this.invArg ();
}
if (!checkMore) {
eval.setShapeSizeBs (20, mad, null);
return;
}var colorArgb =  Clazz.newIntArray (-1, [-2147483648]);
while (++i < this.slen) {
var key = this.paramAsStr (i);
var value = null;
this.getToken (i);
if (!isSet) switch (eval.theTok) {
case 1073742330:
key = "points";
var data =  new Array (3);
data[0] = eval.objectNameParameter (++i);
if (this.chk) continue;
eval.getShapePropertyData (24, "getVertices", data);
value = data;
break;
case 1611272194:
var axes =  new Array (3);
for (var j = 0; j < 3; j++) {
axes[j] =  new JU.V3 ();
axes[j].setT (this.centerParameter (++i));
i = eval.iToken;
}
value = axes;
break;
case 12289:
value = this.centerParameter (++i);
i = eval.iToken;
break;
case 1094713359:
value = Integer.$valueOf (this.intParameter (++i));
break;
case 12291:
value = Boolean.TRUE;
this.checkLength (i + 1);
break;
}
if (value == null) switch (eval.theTok) {
case 1073742335:
key = "on";
value = Boolean.TRUE;
break;
case 1073742334:
key = "on";
value = Boolean.FALSE;
break;
case 1073742138:
value = Float.$valueOf (this.floatParameter (++i));
break;
case 12290:
case 10:
case 1073742325:
key = "atoms";
value = this.atomExpressionAt (i);
i = eval.iToken;
break;
case 1765808134:
case 603979967:
case 1073742074:
translucentLevel = this.getColorTrans (eval, i, true, colorArgb);
i = eval.iToken;
continue;
case 1073742075:
value = this.paramAsStr (++i);
break;
}
if (value == null) this.invArg ();
this.setShapeProperty (20, key.toLowerCase (), value);
}
this.finalizeObject (20, colorArgb[0], translucentLevel, 0, false, null, 0, null);
this.setShapeProperty (20, "thisID", null);
});
Clazz.defineMethod (c$, "image", 
 function () {
if (!this.chk) this.vwr.getConsole ();
var pt = 1;
var id = null;
if (this.tokAt (1) == 1073741974) {
id = this.e.optParameterAsString (++pt);
pt++;
}var fileName = this.e.optParameterAsString (pt);
var isClose = this.e.optParameterAsString (this.slen - 1).equalsIgnoreCase ("close");
if (!isClose && (this.slen == pt || this.slen == pt + 2)) {
var width = (this.slen == pt + 2 ? this.intParameter (pt++) : -1);
var height = (width < 0 ? -1 : this.intParameter (pt));
var params =  new java.util.Hashtable ();
params.put ("fileName", "\1\1" + id);
params.put ("backgroundColor", Integer.$valueOf (this.vwr.getBackgroundArgb ()));
params.put ("type", "png");
params.put ("quality", Integer.$valueOf (-1));
params.put ("width", Integer.$valueOf (width));
params.put ("height", Integer.$valueOf (height));
if (!this.chk) this.vwr.processWriteOrCapture (params);
return;
}pt++;
if (isClose) {
switch (this.slen) {
case 2:
fileName = "closeall";
break;
case 3:
case 4:
break;
default:
this.checkLength (0);
}
}if (!this.chk) this.vwr.fm.loadImage (isClose ? "\1close" : fileName, "\1" + fileName + "\1" + ("".equals (id) || id == null ? null : id), false);
});
Clazz.defineMethod (c$, "invertSelected", 
 function () {
var eval = this.e;
var pt = null;
var plane = null;
var bs = null;
var iAtom = -2147483648;
var ipt = 1;
switch (this.tokAt (1)) {
case 0:
if (this.chk) return;
bs = this.vwr.bsA ();
pt = this.vwr.ms.getAtomSetCenter (bs);
this.vwr.invertAtomCoordPt (pt, bs);
return;
case 528443:
case 1140850689:
ipt++;
case 10:
case 1073742325:
case 12290:
bs = this.atomExpressionAt (ipt);
if (!eval.isAtomExpression (eval.iToken + 1)) {
eval.checkLengthErrorPt (eval.iToken + 1, eval.iToken + 1);
if (!this.chk) {
for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) {
this.vwr.invertRingAt (i, false);
}
}return;
}iAtom = bs.nextSetBit (0);
bs = this.atomExpressionAt (eval.iToken + 1);
break;
case 134217751:
pt = eval.centerParameter (2, null);
break;
case 134217750:
plane = eval.planeParameter (1);
break;
case 134219265:
plane = eval.hklParameter (2);
break;
}
eval.checkLengthErrorPt (eval.iToken + 1, 1);
if (plane == null && pt == null && iAtom == -2147483648) this.invArg ();
if (this.chk) return;
if (iAtom == -1) return;
this.vwr.invertSelected (pt, plane, iAtom, bs);
});
Clazz.defineMethod (c$, "mapProperty", 
 function () {
var bsFrom;
var bsTo;
var property1;
var property2;
var mapKey;
var tokProp1 = 0;
var tokProp2 = 0;
var tokKey = 0;
var eval = this.e;
while (true) {
if (this.tokAt (1) == 1113589787) {
bsFrom = this.vwr.bsA ();
bsTo = this.atomExpressionAt (2);
property1 = property2 = "selected";
} else {
bsFrom = this.atomExpressionAt (1);
if (this.tokAt (++eval.iToken) != 1073742336 || !JS.T.tokAttr (tokProp1 = this.tokAt (++eval.iToken), 1077936128)) break;
property1 = this.paramAsStr (eval.iToken);
bsTo = this.atomExpressionAt (++eval.iToken);
if (this.tokAt (++eval.iToken) != 1073742336 || !JS.T.tokAttr (tokProp2 = this.tokAt (++eval.iToken), 2048)) break;
property2 = this.paramAsStr (eval.iToken);
}if (JS.T.tokAttr (tokKey = this.tokAt (eval.iToken + 1), 1077936128)) mapKey = this.paramAsStr (++eval.iToken);
 else mapKey = JS.T.nameOf (tokKey = 1094715393);
eval.checkLast (eval.iToken);
if (this.chk) return;
var bsOut = null;
this.showString ("mapping " + property1.toUpperCase () + " for " + bsFrom.cardinality () + " atoms to " + property2.toUpperCase () + " for " + bsTo.cardinality () + " atoms using " + mapKey.toUpperCase ());
if (JS.T.tokAttrOr (tokProp1, 1094713344, 1111490560) && JS.T.tokAttrOr (tokProp2, 1094713344, 1111490560) && JS.T.tokAttrOr (tokKey, 1094713344, 1111490560)) {
var data1 = this.getBitsetPropertyFloat (bsFrom, tokProp1 | 224, null, NaN, NaN);
var data2 = this.getBitsetPropertyFloat (bsFrom, tokKey | 224, null, NaN, NaN);
var data3 = this.getBitsetPropertyFloat (bsTo, tokKey | 224, null, NaN, NaN);
var isProperty = (tokProp2 == 1715472409);
var dataOut =  Clazz.newFloatArray (isProperty ? this.vwr.ms.ac : data3.length, 0);
bsOut =  new JU.BS ();
if (data1.length == data2.length) {
var ht =  new java.util.Hashtable ();
for (var i = 0; i < data1.length; i++) {
ht.put (Float.$valueOf (data2[i]), Float.$valueOf (data1[i]));
}
var pt = -1;
var nOut = 0;
for (var i = 0; i < data3.length; i++) {
pt = bsTo.nextSetBit (pt + 1);
var F = ht.get (Float.$valueOf (data3[i]));
if (F == null) continue;
bsOut.set (pt);
dataOut[(isProperty ? pt : nOut)] = F.floatValue ();
nOut++;
}
if (isProperty) this.vwr.setData (property2,  Clazz.newArray (-1, [property2, dataOut, bsOut, Integer.$valueOf (1), Boolean.TRUE]), this.vwr.ms.ac, 0, 0, 2147483647, 0);
 else if (!JS.T.tokAttr (tokProp2, 2048)) this.error (56);
 else this.vwr.setAtomProperty (bsOut, tokProp2, 0, 0, null, dataOut, null);
}}if (bsOut == null) {
var format = "{" + mapKey + "=%[" + mapKey + "]}." + property2 + " = %[" + property1 + "]";
var data = this.getBitsetIdent (bsFrom, format, null, false, 2147483647, false);
var sb =  new JU.SB ();
for (var i = 0; i < data.length; i++) if (data[i].indexOf ("null") < 0) sb.append (data[i]).appendC ('\n');

if (JU.Logger.debugging) JU.Logger.debug (sb.toString ());
var bsSubset = JU.BSUtil.copy (this.vwr.slm.bsSubset);
this.vwr.slm.setSelectionSubset (bsTo);
try {
eval.runScript (sb.toString ());
} catch (e$$) {
if (Clazz.exceptionOf (e$$, Exception)) {
var ex = e$$;
{
this.vwr.slm.setSelectionSubset (bsSubset);
eval.errorStr (-1, "Error: " + ex.getMessage ());
}
} else if (Clazz.exceptionOf (e$$, Error)) {
var er = e$$;
{
this.vwr.slm.setSelectionSubset (bsSubset);
eval.errorStr (-1, "Error: " + er.toString ());
}
} else {
throw e$$;
}
}
this.vwr.slm.setSelectionSubset (bsSubset);
}this.showString ("DONE");
return;
}
this.invArg ();
});
Clazz.defineMethod (c$, "minimize", 
 function () {
var bsSelected = null;
var steps = 2147483647;
var crit = 0;
var addHydrogen = false;
var isSilent = false;
var bsFixed = null;
var isOnly = false;
var minimizer = this.vwr.getMinimizer (false);
for (var i = 1; i < this.slen; i++) switch (this.getToken (i).tok) {
case 1073741828:
addHydrogen = true;
continue;
case 1073741874:
case 1073742162:
this.checkLength (2);
if (this.chk || minimizer == null) return;
minimizer.setProperty (this.paramAsStr (i), null);
return;
case 1073741882:
this.checkLength (2);
if (this.chk || minimizer == null) return;
minimizer.setProperty ("clear", null);
return;
case 1073741894:
if (i != 1) this.invArg ();
var n = 0;
var targetValue = 0;
var aList =  Clazz.newIntArray (5, 0);
if (this.tokAt (++i) == 1073741882) {
this.checkLength (3);
} else {
while (n < 4 && !this.isFloatParameter (i)) {
aList[++n] = this.atomExpressionAt (i).nextSetBit (0);
i = this.e.iToken + 1;
}
aList[0] = n;
if (n == 1) this.invArg ();
targetValue = this.floatParameter (this.e.checkLast (i));
}if (!this.chk) this.vwr.getMinimizer (true).setProperty ("constraint",  Clazz.newArray (-1, [aList,  Clazz.newIntArray (n, 0), Float.$valueOf (targetValue)]));
return;
case 1073741905:
crit = this.floatParameter (++i);
continue;
case 1073741935:
steps = 0;
continue;
case 12293:
if (i != 1) this.invArg ();
bsFixed = this.atomExpressionAt (++i);
if (bsFixed.nextSetBit (0) < 0) bsFixed = null;
i = this.e.iToken;
if (!this.chk) this.vwr.getMinimizer (true).setProperty ("fixed", bsFixed);
if (i + 1 == this.slen) return;
continue;
case 10:
case 1073742325:
isOnly = true;
case 1275082245:
if (this.e.theTok == 1275082245) i++;
bsSelected = this.atomExpressionAt (i);
i = this.e.iToken;
if (this.tokAt (i + 1) == 1073742072) {
i++;
isOnly = true;
}continue;
case 1073742148:
isSilent = true;
break;
case 266298:
steps = this.intParameter (++i);
continue;
default:
this.invArg ();
break;
}

if (!this.chk) try {
this.vwr.minimize (this.e, steps, crit, bsSelected, bsFixed, 0, addHydrogen, isOnly, isSilent, false);
} catch (e1) {
if (Clazz.exceptionOf (e1, Exception)) {
throw  new JS.ScriptInterruption (this.e, "minimize", 1);
} else {
throw e1;
}
}
});
Clazz.defineMethod (c$, "modulation", 
 function () {
var qtOffset = null;
var eval = this.e;
var mod = true;
var isQ = false;
var bs = null;
var i = 1;
switch (this.getToken (i).tok) {
case 1073742334:
mod = false;
case 0:
case 1073742335:
break;
case 12290:
case 10:
case 1073742325:
bs = this.atomExpressionAt (1);
switch (this.tokAt (eval.iToken + 1)) {
case 0:
break;
case 1073742334:
mod = false;
case 1073742335:
eval.iToken++;
break;
}
eval.checkLast (eval.iToken);
break;
case 1073742332:
case 8:
qtOffset = eval.getPoint3f (1, false, true);
isQ = (this.tokAt (eval.iToken + 1) == 1073742335);
break;
default:
var s = eval.theToken.value.toString ();
i++;
if (s.equalsIgnoreCase ("t")) {
eval.theTok = 3;
} else if (s.equalsIgnoreCase ("m") || s.equalsIgnoreCase ("q")) {
eval.theTok = 2;
} else {
this.invArg ();
}case 3:
case 2:
switch (eval.theTok) {
case 3:
if (this.isFloatParameter (i)) {
var t1 = this.floatParameter (i);
qtOffset = JU.P3.new3 (t1, t1, t1);
} else {
qtOffset = eval.getPoint3f (i, false, true);
}break;
case 2:
if (this.tokAt (i) == 2) {
var t = this.intParameter (i);
qtOffset = JU.P3.new3 (t, t, t);
} else {
qtOffset = eval.getPoint3f (i, false, true);
}isQ = true;
break;
}
break;
case 1073742138:
var scale = this.floatParameter (2);
if (!this.chk) this.vwr.setFloatProperty ("modulationScale", scale);
return;
}
if (!this.chk) {
this.vwr.tm.setVibrationPeriod (0);
this.vwr.setModulation (bs, mod, qtOffset, isQ);
}});
Clazz.defineMethod (c$, "mutate", 
 function () {
var bs;
var i;
switch (this.tokAt (1)) {
case 2:
this.st[1] = JS.T.o (4, "" + this.st[1].value);
default:
bs = this.atomExpressionAt (1);
i = ++this.e.iToken;
break;
case 268435633:
bs = this.vwr.getAllAtoms ();
i = 2;
break;
}
bs.and (this.vwr.getModelUndeletedAtomsBitSet (this.vwr.ms.mc - 1));
var iatom = bs.length () - 1;
var imodel = 0;
if (iatom < 0 || (imodel = this.vwr.ms.at[iatom].mi) != this.vwr.ms.mc - 1 || this.vwr.ms.isTrajectory (imodel)) return;
var group = this.e.optParameterAsString (i);
this.e.checkLast (i);
if (this.chk || !this.vwr.ms.am[imodel].isBioModel) return;
var isFile = (this.tokAt (i) == 4 && !group.startsWith ("~"));
var list = null;
if (isFile) {
list =  Clazz.newArray (-1, [group]);
group = null;
} else {
group = JU.PT.replaceAllCharacters (group, ",; \t\n", " ").trim ().toUpperCase ();
var isOneLetter = group.startsWith ("~");
if (isOneLetter || group.length != 3 || !this.vwr.getJBR ().isKnownPDBGroup (group, 20)) group = this.vwr.getJBR ().toStdAmino3 (isOneLetter ? group.substring (1) : group);
list = JU.PT.getTokens (group);
}if (list.length > 0) this.vwr.ms.bioModelset.mutate (bs, group, list);
});
Clazz.defineMethod (c$, "navigate", 
 function () {
var eval = this.e;
if (this.slen == 1) {
eval.setBooleanProperty ("navigationMode", true);
return;
}var rotAxis = JU.V3.new3 (0, 1, 0);
var list =  new JU.Lst ();
var pt;
if (this.slen == 2) {
switch (this.getToken (1).tok) {
case 1073742335:
case 1073742334:
if (this.chk) return;
eval.setObjectMad10 (34, "axes", 10);
this.setShapeProperty (34, "position", JU.P3.new3 (50, 50, 3.4028235E38));
eval.setBooleanProperty ("navigationMode", true);
this.vwr.tm.setNavOn (eval.theTok == 1073742335);
return;
case 1073742162:
if (!this.chk) this.vwr.tm.setNavXYZ (0, 0, 0);
return;
case 8:
case 1112152078:
break;
default:
this.invArg ();
}
}if (!this.chk && !this.vwr.getBoolean (603979889)) eval.setBooleanProperty ("navigationMode", true);
for (var i = 1; i < this.slen; i++) {
var timeSec = (this.isFloatParameter (i) ? this.floatParameter (i++) : 2);
if (timeSec < 0) this.invArg ();
if (!this.chk && timeSec > 0) eval.refresh (false);
switch (this.getToken (i).tok) {
case 8:
case 1073742332:
pt = this.getPoint3f (i, true);
eval.iToken++;
if (eval.iToken != this.slen) this.invArg ();
if (!this.chk) this.vwr.tm.setNavXYZ (pt.x, pt.y, pt.z);
return;
case 554176526:
var depth = this.floatParameter (++i);
if (!this.chk) list.addLast ( Clazz.newArray (-1, [Integer.$valueOf (554176526), Float.$valueOf (timeSec), Float.$valueOf (depth)]));
continue;
case 12289:
pt = this.centerParameter (++i);
i = eval.iToken;
if (!this.chk) list.addLast ( Clazz.newArray (-1, [Integer.$valueOf (134217751), Float.$valueOf (timeSec), pt]));
continue;
case 528432:
switch (this.getToken (++i).tok) {
case 1111492629:
rotAxis.set (1, 0, 0);
i++;
break;
case 1111492630:
rotAxis.set (0, 1, 0);
i++;
break;
case 1111492631:
rotAxis.set (0, 0, 1);
i++;
break;
case 8:
case 1073742332:
rotAxis.setT (this.getPoint3f (i, true));
i = eval.iToken + 1;
break;
case 1073741824:
this.invArg ();
break;
}
var degrees = this.floatParameter (i);
if (!this.chk) list.addLast ( Clazz.newArray (-1, [Integer.$valueOf (528432), Float.$valueOf (timeSec), rotAxis, Float.$valueOf (degrees)]));
continue;
case 4160:
var x = NaN;
var y = NaN;
if (this.isFloatParameter (++i)) {
x = this.floatParameter (i);
y = this.floatParameter (++i);
} else {
switch (this.tokAt (i)) {
case 1111492629:
x = this.floatParameter (++i);
break;
case 1111492630:
y = this.floatParameter (++i);
break;
default:
pt = this.centerParameter (i);
i = eval.iToken;
if (!this.chk) list.addLast ( Clazz.newArray (-1, [Integer.$valueOf (4160), Float.$valueOf (timeSec), pt]));
continue;
}
}if (!this.chk) list.addLast ( Clazz.newArray (-1, [Integer.$valueOf (268435634), Float.$valueOf (timeSec), Float.$valueOf (x), Float.$valueOf (y)]));
continue;
case 268435632:
continue;
case 1112152078:
var pathGuide;
var vp =  new JU.Lst ();
var bs;
if (eval.isAtomExpression (i + 1)) {
bs = this.atomExpressionAt (++i);
i = eval.iToken;
} else {
bs = this.vwr.bsA ();
}if (this.chk) return;
this.vwr.getPolymerPointsAndVectors (bs, vp);
var n;
if ((n = vp.size ()) > 0) {
pathGuide =  new Array (n);
for (var j = 0; j < n; j++) {
pathGuide[j] = vp.get (j);
}
list.addLast ( Clazz.newArray (-1, [Integer.$valueOf (1112152078), Float.$valueOf (timeSec), pathGuide]));
continue;
}break;
case 1073742084:
var path;
var theta = null;
if (this.getToken (i + 1).tok == 1073742330) {
i++;
var pathID = eval.objectNameParameter (++i);
if (this.chk) return;
this.setShapeProperty (22, "thisID", pathID);
path = this.getShapeProperty (22, "vertices");
eval.refresh (false);
if (path == null) this.invArg ();
var indexStart = Clazz.floatToInt (this.isFloatParameter (i + 1) ? this.floatParameter (++i) : 0);
var indexEnd = Clazz.floatToInt (this.isFloatParameter (i + 1) ? this.floatParameter (++i) : 2147483647);
list.addLast ( Clazz.newArray (-1, [Integer.$valueOf (1073742084), Float.$valueOf (timeSec), path, theta,  Clazz.newIntArray (-1, [indexStart, indexEnd])]));
continue;
}var v =  new JU.Lst ();
while (eval.isCenterParameter (i + 1)) {
v.addLast (this.centerParameter (++i));
i = eval.iToken;
}
if (v.size () > 0) {
path = v.toArray ( new Array (v.size ()));
if (!this.chk) list.addLast ( Clazz.newArray (-1, [Integer.$valueOf (1073742084), Float.$valueOf (timeSec), path, theta,  Clazz.newIntArray (-1, [0, 2147483647])]));
continue;
}default:
this.invArg ();
}
}
if (!this.chk && !this.vwr.isJmolDataFrame ()) this.vwr.tm.navigateList (eval, list);
});
Clazz.defineMethod (c$, "plot", 
 function (args) {
var eval = this.e;
var modelIndex = this.vwr.am.cmi;
if (modelIndex < 0) eval.errorStr (30, "plot");
modelIndex = this.vwr.ms.getJmolDataSourceFrame (modelIndex);
var pt = args.length - 1;
var isReturnOnly = (args !== this.st);
var pdbFormat = true;
var statementSave = this.st;
if (isReturnOnly) eval.st = this.st = args;
var tokCmd = (isReturnOnly ? 134222350 : args[0].tok);
var pt0 = (isReturnOnly || tokCmd == 134221850 || tokCmd == 4138 ? 0 : 1);
var filename = null;
var makeNewFrame = true;
var isDraw = false;
switch (tokCmd) {
case 4133:
case 134221850:
case 4138:
break;
case 135176:
makeNewFrame = false;
isDraw = true;
break;
case 134222350:
makeNewFrame = false;
pdbFormat = false;
break;
case 134221856:
makeNewFrame = false;
if (JS.CmdExt.tokAtArray (pt, args) == 4) {
filename = this.stringParameter (pt--);
} else if (JS.CmdExt.tokAtArray (pt - 1, args) == 1073742336) {
filename = this.paramAsStr (pt - 2) + "." + this.paramAsStr (pt);
pt -= 3;
} else {
eval.st = this.st = statementSave;
eval.iToken = this.st.length;
this.error (13);
}eval.slen = this.slen = pt + 1;
break;
}
var qFrame = "";
var parameters = null;
var stateScript = "";
var isQuaternion = false;
var isDerivative = false;
var isSecondDerivative = false;
var isRamachandranRelative = false;
var props =  new Array (3);
var propToks =  Clazz.newIntArray (3, 0);
var bs = JU.BSUtil.copy (this.vwr.bsA ());
var preSelected = "; select " + JU.Escape.eBS (bs) + ";\n ";
var type = eval.optParameterAsString (pt).toLowerCase ();
var minXYZ = null;
var maxXYZ = null;
var format = null;
var tok = JS.CmdExt.tokAtArray (pt0, args);
if (tok == 4) tok = JS.T.getTokFromName (args[pt0].value);
switch (tok) {
default:
eval.iToken = 1;
this.invArg ();
break;
case 134221834:
eval.iToken = 1;
type = "data";
preSelected = "";
break;
case 1715472409:
eval.iToken = pt0 + 1;
for (var i = 0; i < 3; i++) {
switch (this.tokAt (eval.iToken)) {
case 4:
propToks[i] = JS.T.getTokFromName (eval.getToken (eval.iToken).value);
break;
default:
propToks[i] = this.tokAt (eval.iToken);
break;
case 0:
if (i == 0) this.invArg ();
case 1287653388:
case 32:
case 64:
i = 2;
continue;
}
if (propToks[i] != 1715472409 && !JS.T.tokAttr (propToks[i], 1077936128)) this.invArg ();
props[i] = this.getToken (eval.iToken).value.toString ();
eval.iToken++;
}
if (this.tokAt (eval.iToken) == 1287653388) {
format = this.stringParameter (++eval.iToken);
pdbFormat = false;
eval.iToken++;
}if (this.tokAt (eval.iToken) == 32) {
minXYZ = this.getPoint3f (++eval.iToken, false);
eval.iToken++;
}if (this.tokAt (eval.iToken) == 64) {
maxXYZ = this.getPoint3f (++eval.iToken, false);
eval.iToken++;
}type = "property " + props[0] + (props[1] == null ? "" : " " + props[1]) + (props[2] == null ? "" : " " + props[2]);
if (bs.nextSetBit (0) < 0) bs = this.vwr.getModelUndeletedAtomsBitSet (modelIndex);
stateScript = "select " + JU.Escape.eBS (bs) + ";\n ";
break;
case 4138:
if (type.equalsIgnoreCase ("draw")) {
isDraw = true;
type = eval.optParameterAsString (--pt).toLowerCase ();
}isRamachandranRelative = (pt > pt0 && type.startsWith ("r"));
type = "ramachandran" + (isRamachandranRelative ? " r" : "") + (tokCmd == 135176 ? " draw" : "");
break;
case 134221850:
case 136314895:
qFrame = " \"" + this.vwr.getQuaternionFrame () + "\"";
stateScript = "set quaternionFrame" + qFrame + ";\n  ";
isQuaternion = true;
if (type.equalsIgnoreCase ("draw")) {
isDraw = true;
type = eval.optParameterAsString (--pt).toLowerCase ();
}isDerivative = (type.startsWith ("deriv") || type.startsWith ("diff"));
isSecondDerivative = (isDerivative && type.indexOf ("2") > 0);
if (isDerivative) pt--;
if (type.equalsIgnoreCase ("helix") || type.equalsIgnoreCase ("axis")) {
isDraw = true;
isDerivative = true;
pt = -1;
}type = ((pt <= pt0 ? "" : eval.optParameterAsString (pt)) + "w").substring (0, 1);
if (type.equals ("a") || type.equals ("r")) isDerivative = true;
if (!JU.PT.isOneOf (type, ";w;x;y;z;r;a;")) eval.evalError ("QUATERNION [w,x,y,z,a,r] [difference][2]", null);
type = "quaternion " + type + (isDerivative ? " difference" : "") + (isSecondDerivative ? "2" : "") + (isDraw ? " draw" : "");
break;
}
this.st = statementSave;
if (this.chk) return "";
if (makeNewFrame) {
stateScript += "plot " + type;
var ptDataFrame = this.vwr.ms.getJmolDataFrameIndex (modelIndex, stateScript);
if (ptDataFrame > 0 && tokCmd != 134221856 && tokCmd != 134222350) {
this.vwr.setCurrentModelIndexClear (ptDataFrame, true);
return "";
}}var dataX = null;
var dataY = null;
var dataZ = null;
var propData =  new Array (3);
if (tok == 1715472409) {
dataX = this.getBitsetPropertyFloat (bs, propToks[0] | 224, propToks[0] == 1715472409 ? props[0] : null, (minXYZ == null ? NaN : minXYZ.x), (maxXYZ == null ? NaN : maxXYZ.x));
propData[0] = props[0] + " " + JU.Escape.eAF (dataX);
if (props[1] != null) {
dataY = this.getBitsetPropertyFloat (bs, propToks[1] | 224, propToks[1] == 1715472409 ? props[1] : null, (minXYZ == null ? NaN : minXYZ.y), (maxXYZ == null ? NaN : maxXYZ.y));
propData[1] = props[1] + " " + JU.Escape.eAF (dataY);
}if (props[2] != null) {
dataZ = this.getBitsetPropertyFloat (bs, propToks[2] | 224, propToks[2] == 1715472409 ? props[2] : null, (minXYZ == null ? NaN : minXYZ.z), (maxXYZ == null ? NaN : maxXYZ.z));
propData[2] = props[2] + " " + JU.Escape.eAF (dataZ);
}if (minXYZ == null) minXYZ = JU.P3.new3 (this.getPlotMinMax (dataX, false, propToks[0]), this.getPlotMinMax (dataY, false, propToks[1]), this.getPlotMinMax (dataZ, false, propToks[2]));
if (maxXYZ == null) maxXYZ = JU.P3.new3 (this.getPlotMinMax (dataX, true, propToks[0]), this.getPlotMinMax (dataY, true, propToks[1]), this.getPlotMinMax (dataZ, true, propToks[2]));
JU.Logger.info ("plot min/max: " + minXYZ + " " + maxXYZ);
var center = null;
var factors = null;
if (pdbFormat) {
factors = JU.P3.new3 (1, 1, 1);
center =  new JU.P3 ();
center.ave (maxXYZ, minXYZ);
factors.sub2 (maxXYZ, minXYZ);
factors.set (factors.x / 200, factors.y / 200, factors.z / 200);
if (JS.T.tokAttr (propToks[0], 1094713344)) {
factors.x = 1;
center.x = 0;
} else if (factors.x > 0.1 && factors.x <= 10) {
factors.x = 1;
}if (JS.T.tokAttr (propToks[1], 1094713344)) {
factors.y = 1;
center.y = 0;
} else if (factors.y > 0.1 && factors.y <= 10) {
factors.y = 1;
}if (JS.T.tokAttr (propToks[2], 1094713344)) {
factors.z = 1;
center.z = 0;
} else if (factors.z > 0.1 && factors.z <= 10) {
factors.z = 1;
}if (props[2] == null || props[1] == null) center.z = minXYZ.z = maxXYZ.z = factors.z = 0;
for (var i = 0; i < dataX.length; i++) dataX[i] = (dataX[i] - center.x) / factors.x;

if (props[1] != null) for (var i = 0; i < dataY.length; i++) dataY[i] = (dataY[i] - center.y) / factors.y;

if (props[2] != null) for (var i = 0; i < dataZ.length; i++) dataZ[i] = (dataZ[i] - center.z) / factors.z;

}parameters =  Clazz.newArray (-1, [bs, dataX, dataY, dataZ, minXYZ, maxXYZ, factors, center, format, propData]);
}if (tokCmd == 134221856) return this.vwr.writeFileData (filename, "PLOT_" + type, modelIndex, parameters);
var data = (type.equals ("data") ? "1 0 H 0 0 0 # Jmol PDB-encoded data" : this.vwr.getPdbData (modelIndex, type, null, parameters, null, true));
if (tokCmd == 134222350) return data;
if (JU.Logger.debugging) JU.Logger.debug (data);
if (tokCmd == 135176) {
eval.runScript (data);
return "";
}var savedFileInfo = this.vwr.fm.getFileInfo ();
var oldAppendNew = this.vwr.getBoolean (603979792);
this.vwr.g.appendNew = true;
var isOK = (data != null && this.vwr.openStringInlineParamsAppend (data, null, true) == null);
this.vwr.g.appendNew = oldAppendNew;
this.vwr.fm.setFileInfo (savedFileInfo);
if (!isOK) return "";
var modelCount = this.vwr.ms.mc;
this.vwr.ms.setJmolDataFrame (stateScript, modelIndex, modelCount - 1);
if (tok != 1715472409) stateScript += ";\n" + preSelected;
var ss = this.vwr.addStateScript (stateScript, true, false);
var radius = 150;
var script;
switch (tok) {
default:
script = "frame 0.0; frame last; reset;select visible;wireframe only;";
radius = 10;
break;
case 1715472409:
this.vwr.setFrameTitle (modelCount - 1, type + " plot for model " + this.vwr.getModelNumberDotted (modelIndex));
script = "frame 0.0; frame last; reset;select visible; spacefill 3.0; wireframe 0;draw plotAxisX" + modelCount + " {100 -100 -100} {-100 -100 -100} \"" + props[0] + "\";" + "draw plotAxisY" + modelCount + " {-100 100 -100} {-100 -100 -100} \"" + props[1] + "\";";
if (props[2] != null) script += "draw plotAxisZ" + modelCount + " {-100 -100 100} {-100 -100 -100} \"" + props[2] + "\";";
break;
case 4138:
this.vwr.setFrameTitle (modelCount - 1, "ramachandran plot for model " + this.vwr.getModelNumberDotted (modelIndex));
script = "frame 0.0; frame last; reset;select visible; color structure; spacefill 3.0; wireframe 0;draw ramaAxisX" + modelCount + " {100 0 0} {-100 0 0} \"phi\";" + "draw ramaAxisY" + modelCount + " {0 100 0} {0 -100 0} \"psi\";";
break;
case 134221850:
case 136314895:
this.vwr.setFrameTitle (modelCount - 1, type.$replace ('w', ' ') + qFrame + " for model " + this.vwr.getModelNumberDotted (modelIndex));
var color = (JU.C.getHexCode (this.vwr.cm.colixBackgroundContrast));
script = "frame 0.0; frame last; reset;select visible; wireframe 0; spacefill 3.0; isosurface quatSphere" + modelCount + " color " + color + " sphere 100.0 mesh nofill frontonly translucent 0.8;" + "draw quatAxis" + modelCount + "X {100 0 0} {-100 0 0} color red \"x\";" + "draw quatAxis" + modelCount + "Y {0 100 0} {0 -100 0} color green \"y\";" + "draw quatAxis" + modelCount + "Z {0 0 100} {0 0 -100} color blue \"z\";" + "color structure;" + "draw quatCenter" + modelCount + "{0 0 0} scale 0.02;";
break;
}
eval.runScript (script + preSelected);
ss.setModelIndex (this.vwr.am.cmi);
this.vwr.setRotationRadius (radius, true);
eval.sm.loadShape (31);
this.showString ("frame " + this.vwr.getModelNumberDotted (modelCount - 1) + (type.length > 0 ? " created: " + type + (isQuaternion ? qFrame : "") : ""));
return "";
}, "~A");
Clazz.defineMethod (c$, "polyhedra", 
 function () {
var eval = this.e;
var haveBonds = (this.slen == 1);
var haveCenter = false;
var needsGenerating = haveBonds;
var onOffDelete = false;
var typeSeen = false;
var edgeParameterSeen = false;
var scale = NaN;
var nAtomSets = 0;
eval.sm.loadShape (21);
this.setShapeProperty (21, "init", Boolean.TRUE);
var translucentLevel = 3.4028235E38;
var radius = -1;
var colorArgb =  Clazz.newIntArray (-1, [-2147483648]);
var noToParam = -1;
var offset = null;
var id = null;
var ok = false;
var faces = null;
var points = null;
for (var i = 1; i < this.slen; ++i) {
var propertyName = null;
var propertyValue = null;
switch (this.getToken (i).tok) {
case 1073742197:
scale = NaN;
case 1073741872:
var index = (this.e.theTok == 1073742197 ? -1 : (this.tokAt (i + 1) == 2 ? this.intParameter (++i) : 1));
if (!this.chk) (J.api.Interface.getInterface ("JU.BZone", this.vwr, "script")).setViewer (this.vwr).createBZ (index, null, false, id, scale);
this.setShapeProperty (21, "init", Boolean.FALSE);
return;
case 6:
propertyName = "info";
propertyValue = this.e.theToken.value;
needsGenerating = true;
break;
case 134217751:
propertyName = "points";
propertyValue = Float.$valueOf (this.tokAt (++i) == 1073742334 ? 0 : this.e.floatParameter (i));
ok = true;
break;
case 1073742138:
scale = this.floatParameter (++i);
ok = true;
continue;
case 1814695966:
if (id != null) this.invArg ();
propertyName = "unitCell";
propertyValue = Boolean.TRUE;
needsGenerating = true;
break;
case 1073742072:
this.e.restrictSelected (false, false);
eval.theTok = 1073742335;
case 1073742335:
case 12291:
case 1073742334:
if (i + 1 != this.slen || needsGenerating || nAtomSets > 1) this.error (18);
propertyName = (eval.theTok == 1073742334 ? "off" : eval.theTok == 1073742335 ? "on" : "delete");
onOffDelete = true;
break;
case 7:
if (id == null || needsGenerating) this.invArg ();
needsGenerating = true;
faces = this.getIntArray2 (i);
points = this.getAllPoints (eval.iToken + 1);
i = eval.iToken;
if (Clazz.instanceOf (points[0], JM.Atom)) this.setShapeProperty (21, "model", Integer.$valueOf ((points[0]).getModelIndex ()));
propertyName = "definedFaces";
propertyValue =  Clazz.newArray (-1, [faces, points]);
break;
case 1073741961:
propertyName = "full";
break;
case 2:
if (id != null) this.invArg ();
propertyName = "nVertices";
propertyValue = Integer.$valueOf (this.intParameter (i));
needsGenerating = true;
if (this.tokAt (i + 1) == 268435504) i++;
break;
case 1677721602:
if (id != null) this.invArg ();
if (nAtomSets > 0) this.invPO ();
needsGenerating = true;
propertyName = "bonds";
haveBonds = true;
break;
case 1073741852:
if (radius != -1) this.invArg ();
radius = 0;
i--;
case 1665140738:
i++;
case 3:
if (id != null) this.invArg ();
if (nAtomSets > 0) this.invPO ();
propertyName = (radius <= 0 ? "radius" : "radius1");
propertyValue = Float.$valueOf (radius = (radius == 0 ? 0 : this.floatParameter (i)));
needsGenerating = true;
break;
case 1073742066:
if (!this.isFloatParameter (i + 1)) {
offset = this.e.centerParameter (++i, null);
i = eval.iToken;
ok = true;
continue;
}case 1073741937:
this.setShapeProperty (21, "collapsed", null);
case 1073742099:
case 1073741924:
propertyName = JS.T.nameOf (eval.theTok);
switch (this.tokAt (i + 1)) {
case 268435860:
case 268435504:
i++;
break;
}
propertyValue = Float.$valueOf (this.floatParameter (++i));
break;
case 1094717454:
if (id == null) this.invArg ();
propertyName = "model";
propertyValue = Integer.$valueOf (this.intParameter (++i));
break;
case 1073742170:
if (nAtomSets > 1 || id != null && !haveCenter || noToParam == i) this.invPO ();
nAtomSets = 3;
if (eval.isAtomExpression (++i)) {
propertyName = (needsGenerating || haveCenter ? "to" : "toBitSet");
propertyValue = this.atomExpressionAt (i);
} else if (eval.isArrayParameter (i)) {
propertyName = "toVertices";
propertyValue = eval.getPointArray (i, -1, false);
} else {
this.error (19);
}i = eval.iToken;
needsGenerating = true;
break;
case 12290:
case 10:
case 1073742325:
if (typeSeen) this.invPO ();
switch (++nAtomSets) {
case 1:
if (id != null) this.invArg ();
propertyName = "centers";
break;
case 2:
propertyName = "to";
needsGenerating = true;
break;
default:
eval.bad ();
}
propertyValue = this.atomExpressionAt (i);
i = eval.iToken;
needsGenerating = new Boolean (needsGenerating | (i + 1 == this.slen)).valueOf ();
break;
case 1765808134:
case 603979967:
case 1073742074:
translucentLevel = this.getColorTrans (eval, i, true, colorArgb);
i = eval.iToken;
continue;
case 1073741948:
case 1073741886:
if (typeSeen) this.error (18);
typeSeen = true;
if (this.isFloatParameter (i + 1)) this.setShapeProperty (21, "faceCenterOffset", Float.$valueOf (this.floatParameter (++i)));
propertyName = (this.e.theTok == 1073741886 ? "collapsed" : null);
break;
case 1073742044:
case 1073741933:
case 1073741956:
case 1073741934:
if (edgeParameterSeen) this.error (18);
edgeParameterSeen = true;
ok = true;
propertyName = JS.T.nameOf (eval.theTok);
break;
case 1073742182:
case 1073742060:
case 1073741861:
case 1073741958:
case 1073741964:
continue;
case 1073741974:
case 268435633:
case 1073741824:
case 4:
if (!eval.isColorParam (i)) {
if (i != 1) this.invPO ();
id = (eval.theTok == 1073741974 ? this.stringParameter (++i) : eval.optParameterAsString (i));
this.setShapeProperty (21, "thisID", id);
this.setShapeProperty (21, "model", Integer.$valueOf (this.vwr.am.cmi));
if (!eval.isCenterParameter (i + 1)) continue;
propertyName = "center";
propertyValue = this.centerParameter (++i);
i = eval.iToken;
haveCenter = true;
break;
}default:
if (eval.isColorParam (i)) {
colorArgb[0] = eval.getArgbParam (i);
if (eval.isCenterParameter (i)) noToParam = eval.iToken + 1;
i = eval.iToken;
continue;
}this.invArg ();
}
if (propertyName != null) this.setShapeProperty (21, propertyName, propertyValue);
if (onOffDelete) return;
}
if (needsGenerating) {
if (!typeSeen && haveBonds) this.setShapeProperty (21, "bonds", null);
this.setShapeProperty (21, "generate", null);
} else if (!ok) {
this.error (19);
}if (offset != null) this.setShapeProperty (21, "offset", offset);
if (!Float.isNaN (scale)) this.setShapeProperty (21, "scale", Float.$valueOf (scale));
if (colorArgb[0] != -2147483648) this.setShapeProperty (21, "colorThis", Integer.$valueOf (colorArgb[0]));
if (translucentLevel != 3.4028235E38) eval.setShapeTranslucency (21, "", "translucentThis", translucentLevel, null);
this.setShapeProperty (21, "init", Boolean.FALSE);
});
Clazz.defineMethod (c$, "write", 
 function (args) {
var eval = this.e;
var pt = 1;
var pt0 = 1;
var scripts = null;
var msg = null;
var localPath = null;
var remotePath = null;
var type = "SPT";
var isCommand = true;
var showOnly = false;
var isContact = false;
if (args == null) {
args = this.st;
showOnly = (this.vwr.isApplet && !this.vwr.isSignedApplet || !this.vwr.haveAccess (JV.Viewer.ACCESS.ALL) || this.vwr.fm.getPathForAllFiles ().length > 0);
} else {
pt = pt0 = 0;
isCommand = false;
showOnly = !isCommand;
}var tok = JS.CmdExt.tokAtArray (pt, args);
if (tok == 4 && !isCommand) {
var t0 = JS.T.getTokenFromName (JS.SV.sValue (args[0]).toLowerCase ());
if (t0 != null) tok = t0.tok;
}switch (tok) {
case 0:
break;
case 134221850:
case 4138:
case 1715472409:
msg = this.plot (args);
return (showOnly ? msg : this.writeMsg (msg));
case 134222850:
if (eval.isArrayParameter (pt + 1)) {
scripts = eval.stringParameterSet (++pt);
localPath = ".";
remotePath = ".";
pt0 = pt = eval.iToken + 1;
tok = this.tokAt (pt);
}break;
default:
type = JS.SV.sValue (this.tokenAt (pt, args)).toUpperCase ();
}
var driverList = this.vwr.getExportDriverList ();
var data = null;
var argCount = (isCommand ? this.slen : args.length);
var type2 = "";
var val = null;
var tVar = null;
var nVibes = 0;
var sceneType = null;
var isCoord = false;
var bsFrames = null;
var width = -1;
var height = -1;
var isExport = false;
var fileName = null;
var quality = -2147483648;
if (tok != 0 && isCommand && this.slen > 1 && this.tokAt (this.slen - 2) == 1073741848) {
type = this.paramAsStr (this.slen - 1).toUpperCase ();
pt0 = argCount;
argCount -= 2;
tok = 0;
}switch (tok) {
case 0:
break;
case 15:
case 6:
type = "VAR";
tVar = this.tokenAt (pt++, args);
break;
case 1073741984:
type = "INLINE";
data = JS.SV.sValue (this.tokenAt (++pt, args));
pt++;
break;
case 134217762:
type = "PGRP";
pt++;
type2 = JS.SV.sValue (this.tokenAt (pt, args)).toLowerCase ();
if (type2.equals ("draw")) pt++;
break;
case 1073742329:
pt++;
isCoord = true;
break;
case 1073742158:
case 134222850:
val = JS.SV.sValue (this.tokenAt (++pt, args)).toLowerCase ();
while (val.equals ("localpath") || val.equals ("remotepath")) {
if (val.equals ("localpath")) localPath = JS.SV.sValue (this.tokenAt (++pt, args));
 else remotePath = JS.SV.sValue (this.tokenAt (++pt, args));
val = JS.SV.sValue (this.tokenAt (++pt, args)).toLowerCase ();
}
type = "SPT";
break;
case 1228935687:
case 134320141:
case 1610616855:
case 135180:
case 1073742015:
case 1073742018:
case 1073877011:
case 1073877010:
case 135188:
pt++;
break;
case 1073741991:
type = "ZIPALL";
pt++;
break;
case 36868:
type = "VAR";
pt += 2;
break;
case 4115:
case 4120:
case 1073742139:
case 4166:
case 1073741824:
case 4:
switch (tok) {
case 4115:
var bsAtoms;
if (pt + 1 < argCount && args[++pt].tok == 1073742325 || args[pt].tok == 10) {
bsAtoms = eval.atomExpression (args, pt, 0, true, false, null, true);
pt = eval.iToken + 1;
} else {
bsAtoms = this.vwr.getAllAtoms ();
}if (!this.chk) bsFrames = this.vwr.ms.getModelBS (bsAtoms, true);
break;
case 4120:
type = "IMAGE";
pt++;
break;
case 1073742139:
val = JS.SV.sValue (this.tokenAt (++pt, args)).toUpperCase ();
if (JU.PT.isOneOf (val, ";PNG;PNGJ;")) {
sceneType = val;
pt++;
} else {
sceneType = "PNG";
}break;
case 4166:
nVibes = eval.intParameterRange (++pt, 1, 10);
if (nVibes == 2147483647) return "";
if (!this.chk) {
this.vwr.tm.setVibrationPeriod (0);
if (!eval.isJS) eval.delayScript (100);
}pt++;
break;
default:
tok = 4120;
break;
}
if (tok == 4120 && pt < args.length) {
var t = JS.T.getTokenFromName (JS.SV.sValue (args[pt]).toLowerCase ());
if (t != null) type = JS.SV.sValue (t).toUpperCase ();
if (JU.PT.isOneOf (type, driverList.toUpperCase ())) {
pt++;
type = type.substring (0, 1).toUpperCase () + type.substring (1).toLowerCase ();
isExport = true;
if (isCommand) fileName = "Jmol." + type.toLowerCase ();
break;
} else if (JU.PT.isOneOf (type, ";ZIP;ZIPALL;SPT;STATE;")) {
pt++;
break;
} else {
type = "IMAGE";
}}if (JS.CmdExt.tokAtArray (pt, args) == 2) {
width = JS.SV.iValue (this.tokenAt (pt++, args));
if (width <= 0) this.invArg ();
height = JS.SV.iValue (this.tokenAt (pt++, args));
if (height <= 0) this.invArg ();
}break;
}
if (pt0 < argCount) {
val = JS.SV.sValue (this.tokenAt (pt, args));
if (val.equalsIgnoreCase ("clipboard")) {
if (this.chk) return "";
} else if (JU.PT.isOneOf (val.toLowerCase (), ";jpg;jpeg;jpg64;jpeg64;gif;gift;pdf;ppm;png;pngj;pngt;")) {
if (JS.CmdExt.tokAtArray (pt + 1, args) == 2 && JS.CmdExt.tokAtArray (pt + 2, args) == 2) {
width = JS.SV.iValue (this.tokenAt (++pt, args));
if (width <= 0) this.invArg ();
height = JS.SV.iValue (this.tokenAt (++pt, args));
if (height <= 0) this.invArg ();
}if (JS.CmdExt.tokAtArray (pt + 1, args) == 2) quality = JS.SV.iValue (this.tokenAt (++pt, args));
} else if (JU.PT.isOneOf (val.toLowerCase (), ";xyz;xyzrn;xyzvib;mol;mol67;sdf;v2000;v3000;json;pdb;pqr;cml;cif;qcjson;")) {
type = val.toUpperCase ();
if (pt + 1 == argCount) pt++;
}if (type.equals ("IMAGE") && JU.PT.isOneOf (val.toLowerCase (), ";jpg;jpeg;jpg64;jpeg64;gif;gift;pdf;ppm;png;pngj;pngt;scene;")) {
type = val.toUpperCase ();
quality = -2147483648;
pt++;
}}if (pt + 2 == argCount) {
var s = JS.SV.sValue (this.tokenAt (++pt, args));
if (s.length > 0 && s.charAt (0) != '.') {
if (val == null) {
System.out.println ("??");
type = val.toUpperCase ();
}}}switch (JS.CmdExt.tokAtArray (pt, args)) {
case 0:
showOnly = true;
break;
case 1073741884:
break;
case 805306401:
fileName = (type.equals ("IMAGE") ? "?jmol.png" : "?jmol." + type.toLowerCase ());
break;
case 1073741824:
case 4:
fileName = JS.SV.sValue (this.tokenAt (pt, args));
if (fileName.equalsIgnoreCase ("clipboard") || !this.vwr.haveAccess (JV.Viewer.ACCESS.ALL)) fileName = null;
break;
default:
this.invArg ();
}
if (type.equals ("IMAGE") || type.equals ("FRAME") || type.equals ("VIBRATION")) {
type = (fileName != null && fileName.indexOf (".") >= 0 ? fileName.substring (fileName.lastIndexOf (".") + 1).toUpperCase () : "JPG");
}if (type.equals ("ISOSURFACE") || type.equals ("CONTACT")) {
isContact = type.equals ("CONTACT");
type = (fileName != null && fileName.indexOf (".") >= 0 ? fileName.substring (fileName.lastIndexOf (".") + 1).toUpperCase () : "JVXL");
if (type.equals ("PMESH")) type = "ISOMESH";
 else if (type.equals ("PMB")) type = "ISOMESHBIN";
}var isImage = JU.PT.isOneOf (type.toLowerCase (), ";jpg;jpeg;jpg64;jpeg64;gif;gift;pdf;ppm;png;pngj;pngt;scene;");
if (!isImage) {
if (type.equals ("MNU")) {
type = "MENU";
} else if (type.equals ("WRL") || type.equals ("VRML")) {
type = "Vrml";
isExport = true;
} else if (type.equals ("X3D")) {
type = "X3d";
isExport = true;
} else if (type.equals ("STL")) {
type = "Stl";
isExport = true;
} else if (type.equals ("IDTF")) {
type = "Idtf";
isExport = true;
} else if (type.equals ("MA")) {
type = "Maya";
isExport = true;
} else if (type.equals ("JS")) {
type = "Js";
isExport = true;
} else if (type.equals ("OBJ")) {
type = "Obj";
isExport = true;
} else if (type.equals ("JVXL")) {
type = "ISOSURFACE";
} else if (type.equals ("XJVXL")) {
type = "ISOSURFACE";
} else if (type.equals ("JMOL")) {
type = "ZIPALL";
} else if (type.equals ("HIS")) {
type = "HISTORY";
}if (type.equals ("COORD") || type.equals ("COORDS")) type = (fileName != null && fileName.indexOf (".") >= 0 ? fileName.substring (fileName.lastIndexOf (".") + 1).toUpperCase () : "XYZ");
}if (scripts != null) {
if (type.equals ("PNG")) type = "PNGJ";
if (!type.equals ("PNGJ") && !type.equals ("ZIPALL") && !type.equals ("ZIP")) this.invArg ();
}if (!isImage && !isExport && !JU.PT.isOneOf (type, ";SCENE;JMOL;ZIP;ZIPALL;SPT;HISTORY;MO;NBO;ISOSURFACE;MESH;PMESH;PMB;ISOMESHBIN;ISOMESH;VAR;FILE;FUNCTION;CFI;CIF;CML;JSON;XYZ;XYZRN;XYZVIB;MENU;MOL;MOL67;PDB;PGRP;PQR;QUAT;RAMA;SDF;V2000;V3000;QCJSON;INLINE;")) eval.errorStr2 (54, "COORDS|FILE|FUNCTIONS|HISTORY|IMAGE|INLINE|ISOSURFACE|JMOL|MENU|MO|NBO|POINTGROUP|QUATERNION [w,x,y,z] [derivative]|RAMACHANDRAN|SPT|STATE|VAR x|ZIP|ZIPALL  CLIPBOARD", "CIF|CML|CFI|GIF|GIFT|JPG|JPG64|JMOL|JVXL|MESH|MOL|PDB|PMESH|PNG|PNGJ|PNGT|PPM|PQR|SDF|CD|JSON|QCJSON|V2000|V3000|SPT|XJVXL|XYZ|XYZRN|XYZVIB|ZIP" + driverList.toUpperCase ().$replace (';', '|'));
if (this.chk) return "";
var fullPath =  new Array (1);
var params;
var timeMsg = this.vwr.getBoolean (603979934);
if (isExport) {
if (timeMsg) JU.Logger.startTimer ("export");
var eparams =  new java.util.Hashtable ();
eparams.put ("type", type);
if (fileName != null) eparams.put ("fileName", fileName);
if (isCommand || fileName != null) eparams.put ("fullPath", fullPath);
eparams.put ("width", Integer.$valueOf (width));
eparams.put ("height", Integer.$valueOf (height));
data = this.vwr.generateOutputForExport (eparams);
if (data == null || data.length == 0) return "";
if (showOnly) return data;
if (!type.equals ("Povray") && !type.equals ("Idtf") || fullPath[0] == null) return this.writeMsg (data);
var ext = (type.equals ("Idtf") ? ".tex" : ".ini");
fileName = fullPath[0] + ext;
params =  new java.util.Hashtable ();
params.put ("fileName", fileName);
params.put ("type", ext);
params.put ("text", data);
params.put ("fullPath", fullPath);
msg = this.vwr.processWriteOrCapture (params);
if (type.equals ("Idtf")) data = data.substring (0, data.indexOf ("\\begin{comment}"));
data = "Created " + fullPath[0] + ":\n\n" + data;
if (timeMsg) this.showString (JU.Logger.getTimerMsg ("export", 0));
if (msg != null) {
var isError = !msg.startsWith ("OK");
if (isError) eval.evalError (msg, null);
eval.report (data, isError);
}return "";
}var bytes = null;
var writeFileData = false;
if (data == null) {
var len = 0;
data = type.intern ();
if (data === "MENU") {
data = this.vwr.getMenu ("");
} else if (data === "PGRP") {
data = this.vwr.ms.getPointGroupAsString (this.vwr.bsA (), null, 0, 1.0, null, null, type2.equals ("draw") ? "" : null);
} else if (data === "PDB" || data === "PQR") {
if (showOnly) {
data = this.vwr.getPdbAtomData (null, null, (data === "PQR"), isCoord);
} else {
writeFileData = true;
type = "PDB_" + data + "-coord " + isCoord;
}} else if (data === "FILE") {
if ("?".equals (fileName)) fileName = "?Jmol." + this.vwr.getP ("_fileType");
if (showOnly) data = this.vwr.getCurrentFileAsString ("script");
 else writeFileData = true;
} else if (data === "CIF" || data === "SDF" || data === "MOL" || data === "MOL67" || data === "V2000" || data === "V3000" || data === "CD" || data === "JSON" || data === "XYZ" || data === "XYZRN" || data === "XYZVIB" || data === "CML" || data === "QCJSON") {
var selected = this.vwr.bsA ();
var bsModel;
msg = " (" + selected.cardinality () + " atoms)";
if (this.vwr.am.cmi >= 0 && !selected.equals (bsModel = this.vwr.getModelUndeletedAtomsBitSet (this.vwr.am.cmi))) msg += "\nNote! Selected atom set " + selected + " is not the same as the current model " + bsModel;
data = this.vwr.getModelExtract (selected, isCoord, false, data);
if (data.startsWith ("ERROR:")) bytes = data;
} else if (data === "CFI") {
data = this.vwr.getModelFileData ("selected", "cfi", false);
} else if (data === "FUNCTION") {
data = this.vwr.getFunctionCalls (null);
type = "TXT";
} else if (data === "VAR") {
if (tVar == null) {
tVar = eval.getParameter (JS.SV.sValue (this.tokenAt (isCommand ? 2 : 1, args)), 1073742190, true);
}var v = null;
if (tVar.tok == 15) {
v =  new JU.Lst ();
v.addLast ((tVar.value).data);
} else if (tVar.tok == 6) {
v = (fileName == null ?  new JU.Lst () : this.prepareBinaryOutput (tVar));
}if (v == null) {
data = tVar.asString ();
type = "TXT";
} else {
if (fileName != null) {
params =  new java.util.Hashtable ();
params.put ("data", v);
if ((bytes = data = this.vwr.createZip (fileName, v.size () == 1 || fileName.endsWith (".png") || fileName.endsWith (".pngj") ? "BINARY" : "ZIPDATA", params)) == null) eval.evalError ("#CANCELED#", null);
}}} else if (data === "SPT") {
if (isCoord) {
var tainted = this.vwr.ms.getTaintedAtoms (2);
this.vwr.setAtomCoordsRelative (JU.P3.new3 (0, 0, 0), null);
data = this.vwr.getStateInfo ();
this.vwr.ms.setTaintedAtoms (tainted, 2);
} else {
data = this.vwr.getStateInfo ();
if (localPath != null || remotePath != null) data = JV.FileManager.setScriptFileReferences (data, localPath, remotePath, null);
}} else if (data === "ZIP" || data === "ZIPALL") {
if (fileName != null) {
params =  new java.util.Hashtable ();
if (scripts != null) params.put ("data", scripts);
if ((bytes = data = this.vwr.createZip (fileName, type, params)) == null) eval.evalError ("#CANCELED#", null);
}} else if (data === "HISTORY") {
data = this.vwr.getSetHistory (2147483647);
type = "SPT";
} else if (data === "MO" || data === "NBO") {
data = this.getMoJvxl (2147483647, data === "NBO");
type = "XJVXL";
} else if (data === "PMESH" || data === "PMB") {
if ((data = this.getIsosurfaceJvxl (29, data)) == null) this.error (31);
type = "XJVXL";
} else if (data === "ISOMESH") {
if ((data = this.getIsosurfaceJvxl (24, data)) == null) this.error (31);
type = "PMESH";
} else if (data === "ISOMESHBIN") {
if ((bytes = this.getIsosurfaceJvxl (24, "ISOMESHBIN")) == null) this.error (31);
type = "PMB";
} else if (data === "ISOSURFACE" || data === "MESH") {
if ((data = this.getIsosurfaceJvxl (isContact ? 25 : 24, data)) == null) this.error (31);
type = (data.indexOf ("<?xml") >= 0 ? "XJVXL" : "JVXL");
if (!showOnly) this.showString (this.getShapeProperty (isContact ? 25 : 24, "jvxlFileInfo"));
} else {
if (isCommand && showOnly && fileName == null) {
showOnly = false;
fileName = "\1";
}len = -1;
if (sceneType == null && quality < 0) quality = -1;
}if (data == null) data = "";
if (len == 0) len = (bytes == null ? data.length : Clazz.instanceOf (bytes, String) ? (bytes).length : (bytes).length);
}if (!isCommand) return data;
if (showOnly) {
eval.showStringPrint (data, true);
return "";
}if (bytes != null && Clazz.instanceOf (bytes, String)) return this.writeMsg (bytes);
if (writeFileData) return this.writeMsg (this.vwr.writeFileData (fileName, type, 0, null));
if (type.equals ("SCENE")) bytes = sceneType;
 else if (bytes == null && (!isImage || fileName != null)) bytes = data;
if (timeMsg) JU.Logger.startTimer ("write");
if (isImage) {
eval.refresh (false);
if (width < 0) width = this.vwr.getScreenWidth ();
if (height < 0) height = this.vwr.getScreenHeight ();
}params =  new java.util.Hashtable ();
if (fileName != null) params.put ("fileName", fileName);
params.put ("backgroundColor", Integer.$valueOf (this.vwr.getBackgroundArgb ()));
params.put ("type", type);
if (Clazz.instanceOf (bytes, String) && quality == -2147483648) params.put ("text", bytes);
 else if (Clazz.instanceOf (bytes, Array)) params.put ("bytes", bytes);
if (scripts != null) params.put ("scripts", scripts);
if (bsFrames != null) params.put ("bsFrames", bsFrames);
params.put ("fullPath", fullPath);
params.put ("quality", Integer.$valueOf (quality));
params.put ("width", Integer.$valueOf (width));
params.put ("height", Integer.$valueOf (height));
params.put ("nVibes", Integer.$valueOf (nVibes));
var ret = this.vwr.processWriteOrCapture (params);
if (ret == null) ret = "canceled";
if (isImage && ret.startsWith ("OK")) ret += "; width=" + width + "; height=" + height;
if (timeMsg) this.showString (JU.Logger.getTimerMsg ("write", 0));
return this.writeMsg (ret + (msg == null ? "" : msg));
}, "~A");
Clazz.defineMethod (c$, "prepareBinaryOutput", 
function (tvar) {
var m = tvar.getMap ();
if (m == null || !m.containsKey ("$_BINARY_$")) return null;
var v =  new JU.Lst ();
for (var e, $e = m.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) {
var key = e.getKey ();
if (key.equals ("$_BINARY_$")) continue;
var o = e.getValue ();
var bytes = (o.tok == 15 ? (o.value).data : null);
if (bytes == null) {
var s = o.asString ();
bytes = (s.startsWith (";base64,") ? JU.Base64.decodeBase64 (s) : s.getBytes ());
}if (key.equals ("_DATA_")) {
v =  new JU.Lst ();
v.addLast (bytes);
return v;
} else if (key.equals ("_IMAGE_")) {
v.add (0, key);
v.add (1, null);
v.add (2, bytes);
} else {
v.addLast (key);
v.addLast (null);
v.addLast (bytes);
}}
return v;
}, "JS.SV");
Clazz.defineMethod (c$, "writeMsg", 
 function (msg) {
if (this.chk || msg == null) return "";
var isError = !msg.startsWith ("OK");
if (isError) {
this.e.evalError (msg, null);
{
alert(msg);
}}this.e.report (msg, isError);
return msg;
}, "~S");
Clazz.defineMethod (c$, "show", 
 function () {
var eval = this.e;
var value = null;
var str = this.paramAsStr (1);
var filter = null;
var filterLen = 0;
if (this.slen > 2 && this.tokAt (this.slen - 2) == 268435632) {
filter = "/" + this.paramAsStr (this.slen - 1);
this.slen -= 2;
filterLen = 2;
} else if ((filter = this.paramAsStr (this.slen - 1)).lastIndexOf ("/") == 0) {
this.slen--;
filterLen = 1;
} else {
filter = null;
}var msg = null;
var name = null;
var len = 2;
var token = this.getToken (1);
var tok = (Clazz.instanceOf (token, JS.SV) && token.tok != 1073741824 ? 0 : token.tok);
if (tok == 4) {
token = JS.T.getTokenFromName (str.toLowerCase ());
if (token != null) tok = token.tok;
}if (tok != 1296041986 && tok != 1073742158 && tok != 1715472409 && tok != 1228935687) this.checkLength (-3);
if (this.slen == 2 && str.indexOf ("?") >= 0) {
msg = this.vwr.getAllSettings (str.substring (0, str.indexOf ("?")));
tok = -1;
}switch (tok) {
case -1:
break;
case 0:
if (!this.chk) msg = (eval.theToken).escape ();
break;
case 1073741925:
eval.checkLength23 ();
len = this.st.length;
if (!this.chk) {
var d = this.vwr.getModelInfo ("domains");
if (Clazz.instanceOf (d, JS.SV)) msg = this.vwr.getAnnotationInfo (d, eval.optParameterAsString (2), 1073741925);
 else msg = "domain information has not been loaded";
}break;
case 1715472409:
msg = this.plot (this.st);
len = this.st.length;
break;
case 1073742189:
eval.checkLength23 ();
len = this.st.length;
if (!this.chk) {
var d = this.vwr.getModelInfo ("validation");
if (Clazz.instanceOf (d, JS.SV)) msg = this.vwr.getAnnotationInfo (d, eval.optParameterAsString (2), 1073742189);
 else msg = "validation information has not been loaded";
}break;
case 134221829:
if (!this.chk) msg = JU.Escape.e (this.vwr.fm.cacheList ());
break;
case 1111490587:
eval.checkLength23 ();
len = this.st.length;
if (!this.chk) {
var d = this.vwr.getModelInfo ("dssr");
msg = (d == null ? "no DSSR information has been read" : len > 2 ? JS.SV.getVariable (this.vwr.extractProperty (d, this.stringParameter (2), -1)).asString () : "" + JS.SV.getVariable (d).asString ());
}break;
case 1073741915:
var version = 2;
if (this.slen == 3) version = (Clazz.floatToInt (this.floatParameter ((len = 3) - 1)));
 else this.checkLength (2 + filterLen);
if (!this.chk) msg = this.vwr.calculateStructures (null, true, false, version);
break;
case 545259572:
this.checkLength (2 + filterLen);
if (!this.chk) msg = this.vwr.fm.getPathForAllFiles ();
break;
case 1275203608:
if (!this.chk) {
var info =  new Array (2);
this.vwr.shm.getShapePropertyData (21, "allInfo", info);
msg = JS.SV.getVariable (info[1]).asString ();
}break;
case 1073742038:
{
if (!this.chk) this.vwr.getNMRPredict (eval.optParameterAsString (2));
return;
}case 1073741929:
case 1073741879:
case 134218757:
this.checkLength ((tok == 1073741879 || tok == 134218757 && this.tokAt (2) == 1073742335 ? len = 3 : 2) + filterLen);
if (this.chk) return;
var param2 = eval.optParameterAsString (2);
if (tok == 1073741879) {
if ("mf".equals (param2)) param2 = "formula";
if ("formula".equals (param2)) {
msg = this.vwr.getModelInfo ("formula");
if (msg != null) msg = JU.PT.rep (msg, " ", "");
}}if (msg == null) {
try {
if (tok != 134218757) {
msg = this.vwr.ms.getModelDataBaseName (this.vwr.bsA ());
if (msg != null && (msg.startsWith ("$") || msg.startsWith (":"))) {
msg = msg.substring (1);
} else {
msg = null;
}} else if (param2.equalsIgnoreCase ("true")) {
msg = this.vwr.getBioSmiles (null);
filter = null;
} else if (filter != null) {
msg = this.vwr.getSmilesOpt (null, -1, -1, 1, filter + "///");
filter = null;
}if (msg == null) {
var level = JU.Logger.getLogLevel ();
JU.Logger.setLogLevel (4);
msg = (tok == 134218757 ? this.vwr.getSmiles (null) : this.vwr.getOpenSmiles (null));
JU.Logger.setLogLevel (level);
}} catch (ex) {
if (Clazz.exceptionOf (ex, Exception)) {
msg = ex.getMessage ();
if (msg == null) {
msg = "";
}ex.printStackTrace ();
} else {
throw ex;
}
}
switch (tok) {
case 134218757:
break;
case 1073741929:
if (msg.length > 0) {
this.vwr.fm.loadImage (this.vwr.setLoadFormat ("_" + msg, '2', false), "\1" + msg, false);
return;
}msg = "Could not show drawing -- Either insufficient atoms are selected or the model is a PDB file.";
break;
case 1073741879:
len = 3;
if (msg.length > 0) {
msg = this.vwr.getChemicalInfo (msg, param2, this.vwr.bsA ());
if (msg.indexOf ("FileNotFound") >= 0) msg = "?";
} else {
msg = "Could not show name -- Either insufficient atoms are selected or the model is a PDB file.";
}}
}break;
case 1073742152:
case 1296041986:
msg = "";
var info = null;
if ((len = this.slen) == 2) {
if (this.chk) break;
info = this.vwr.getSymTemp ().getSpaceGroupInfo (this.vwr.ms, null, -1, false);
} else if (tok == 1073742152) {
var sg = this.paramAsStr (2);
len = 3;
if (this.chk) break;
info = this.vwr.getSymTemp ().getSpaceGroupInfo (this.vwr.ms, JU.PT.rep (sg, "''", "\""), -1, false);
}if (info != null) {
msg = (tok == 1073742152 ? "" + info.get ("spaceGroupInfo") + info.get ("spaceGroupNote") : "") + info.get ("symmetryInfo");
break;
}var iop = (this.tokAt (2) == 2 ? this.intParameter (2) : 0);
var xyz = (this.tokAt (2) == 4 ? this.paramAsStr (2) : null);
var pt1 = null;
var pt2 = null;
var nth = -1;
if (this.slen > 3 && this.tokAt (3) != 4) {
var ret =  Clazz.newArray (-1, [null, this.vwr.getFrameAtoms ()]);
pt1 = eval.centerParameter (2 + (iop == 0 ? 0 : 1), ret);
if (ret[0] != null && ret[0].cardinality () == 0) {
len = this.slen;
break;
}ret[0] = null;
if (iop == 0) {
pt2 = eval.centerParameter (++eval.iToken, ret);
if (ret[0] != null && ret[0].cardinality () == 0) {
len = this.slen;
break;
}}if (this.tokAt (eval.iToken + 1) == 2) nth = eval.getToken (++eval.iToken).intValue;
}var type = (eval.iToken > 1 && this.tokAt (eval.iToken + 1) == 4 ? this.stringParameter (++eval.iToken) : null);
this.checkLength ((len = ++eval.iToken) + filterLen);
if (!this.chk) {
var o = this.vwr.getSymTemp ().getSymmetryInfoAtom (this.vwr.ms, this.vwr.getAllAtoms ().nextSetBit (0), xyz, iop, pt1, pt2, type, 0, 0, nth);
msg = (Clazz.instanceOf (o, java.util.Map) ? JS.SV.getVariable (o).asString () : o.toString ());
}break;
case 1648363544:
var vdwType = null;
if (this.slen > 2) {
len = this.slen;
vdwType = J.c.VDW.getVdwType (this.paramAsStr (2));
if (vdwType == null) this.invArg ();
}if (!this.chk) msg = this.vwr.getDefaultVdwNameOrData (0, vdwType, null);
break;
case 134320141:
eval.checkLength23 ();
len = this.slen;
var s = eval.optParameterAsString (2);
var pt;
if (filter == null && (pt = s.indexOf ('/')) >= 0) {
filter = s.substring (pt + 1);
s = s.substring (0, pt);
}if (!this.chk) msg = this.vwr.getFunctionCalls (s);
break;
case 36867:
this.checkLength (2 + filterLen);
if (!this.chk) msg = this.vwr.getAllSettings (null);
break;
case 1073742166:
msg = this.vwr.getFrameTitle ();
break;
case 1073742184:
if ((len = this.slen) == 2) {
if (!this.chk) this.vwr.showUrl (eval.getFullPathName ());
} else {
name = this.paramAsStr (2);
if (!this.chk) this.vwr.showUrl (name);
}return;
case 1765808134:
str = "defaultColorScheme";
break;
case 1610612740:
str = "scaleAngstromsPerInch";
break;
case 134221850:
case 4138:
if (this.chk) return;
var modelIndex = this.vwr.am.cmi;
if (modelIndex < 0) eval.errorStr (30, "show " + eval.theToken.value);
msg = this.plot (this.st);
len = this.slen;
break;
case 14:
case 1112152078:
if (!this.chk) msg = this.getContext (false);
break;
case 1073741888:
name = eval.optParameterAsString (2);
if (name.length > 0) len = 3;
if (!this.chk) value = this.vwr.cm.getColorSchemeList (name);
break;
case 1073742192:
if (!this.chk) msg = this.vwr.getAtomDefs (this.vwr.definedAtomSets) + this.vwr.g.getVariableList () + this.getContext (true);
break;
case 536870926:
if (!this.chk) msg = this.vwr.getTrajectoryState ();
break;
case 553648147:
value = "" + JS.ScriptEval.commandHistoryLevelMax;
break;
case 553648150:
value = "" + JU.Logger.getLogLevel ();
break;
case 603979825:
value = "" + this.vwr.getBoolean (603979825);
break;
case 553648178:
msg = "set strandCountForStrands " + this.vwr.getStrandCount (12) + "; set strandCountForMeshRibbon " + this.vwr.getStrandCount (13);
break;
case 536875070:
msg = this.vwr.showTimeout ((len = this.slen) == 2 ? null : this.paramAsStr (2));
break;
case 536870918:
value = JU.Escape.eP (this.vwr.getDefaultLattice ());
break;
case 4126:
if (!this.chk) msg = this.vwr.getMinimizationInfo ();
break;
case 1611272194:
switch (this.vwr.g.axesMode) {
case 603979808:
msg = "set axesUnitcell";
break;
case 603979804:
msg = "set axesMolecular";
break;
default:
msg = "set axesWindow";
}
break;
case 1610612737:
msg = "set bondMode " + (this.vwr.getBoolean (603979812) ? "OR" : "AND");
break;
case 1649022989:
if (!this.chk) msg = "set strandCountForStrands " + this.vwr.getStrandCount (12) + "; set strandCountForMeshRibbon " + this.vwr.getStrandCount (13);
break;
case 1613238294:
msg = "set hbondsBackbone " + this.vwr.getBoolean (603979852) + ";set hbondsSolid " + this.vwr.getBoolean (603979854);
break;
case 1611141175:
if (!this.chk) msg = this.vwr.getSpinState ();
break;
case 1611141176:
msg = "set ssbondsBackbone " + this.vwr.getBoolean (603979952);
break;
case 1610625028:
case 1611141171:
msg = "selectionHalos " + (this.vwr.getSelectionHalosEnabled () ? "ON" : "OFF");
break;
case 1612709894:
msg = "set selectHetero " + this.vwr.getBoolean (1612709894);
break;
case 1073741828:
msg = JU.Escape.eAP (this.vwr.getAdditionalHydrogens (null, true, true, null));
break;
case 1612709900:
msg = "set selectHydrogens " + this.vwr.getBoolean (1612709900);
break;
case 553648130:
case 553648141:
case 536870924:
case 553648176:
case 553648172:
case 1073741995:
if (!this.chk) msg = this.vwr.getLightingState ();
break;
case 1073742136:
case 4146:
if (!this.chk) msg = this.vwr.stm.listSavedStates ();
break;
case 1814695966:
if (!this.chk) msg = this.vwr.getUnitCellInfoText ();
break;
case 1073742329:
if ((len = this.slen) == 2) {
if (!this.chk) msg = this.vwr.getCoordinateState (this.vwr.bsA ());
break;
}var nameC = this.paramAsStr (2);
if (!this.chk) msg = this.vwr.stm.getSavedCoordinates (nameC);
break;
case 1073742158:
if (!this.chk && eval.outputBuffer == null) this.vwr.sm.clearConsole ();
if ((len = this.slen) == 2) {
if (!this.chk) msg = this.vwr.getStateInfo ();
break;
}if (filter != null && this.slen == 3) {
if (!this.chk) msg = this.vwr.getStateInfo ();
break;
} else if (this.tokAt (2) == 1228935687 && (len = this.slen) == 4) {
if (!this.chk) msg = this.vwr.fm.getEmbeddedFileState (this.paramAsStr (3), true, "state.spt");
break;
}len = 3;
name = this.paramAsStr (2);
if (!this.chk) msg = this.vwr.stm.getSavedState (name);
break;
case 1639976963:
if ((len = this.slen) == 2) {
if (!this.chk) msg = this.vwr.ms.getProteinStructureState (this.vwr.bsA (), 134222350);
break;
}var shape = this.paramAsStr (2);
if (!this.chk) msg = this.vwr.stm.getSavedStructure (shape);
break;
case 134221834:
var dtype = ((len = this.slen) == 3 ? this.paramAsStr (2) : null);
if (!this.chk) {
var data = this.vwr.getDataObj (dtype, null, -2);
msg = (data == null ? "no data" : JU.Escape.encapsulateData (data[0], data[1], (data[3]).intValue ()));
}break;
case 1073742330:
len = 3;
msg = eval.setObjectProperty ();
break;
case 1678381065:
if (!this.chk) {
msg = this.vwr.ms.getBoundBoxCommand (true);
}break;
case 12289:
if (!this.chk) msg = "center " + JU.Escape.eP (this.vwr.tm.fixedRotationCenter);
break;
case 135176:
if (!this.chk) msg = this.getShapeProperty (22, "command");
break;
case 1228935687:
if (this.slen == 2) {
if (!this.chk) {
if (filter == null) this.vwr.sm.clearConsole ();
msg = this.vwr.getCurrentFileAsString ("script");
}if (msg == null) msg = "<unavailable>";
break;
}len = 3;
value = this.paramAsStr (2);
if (!this.chk) {
if (filter == null) this.vwr.sm.clearConsole ();
msg = this.vwr.getFileAsString3 (value, true, null);
}break;
case 4115:
if (this.tokAt (2) == 1073742327 && (len = 3) > 0) msg = this.vwr.getModelFileInfoAll ();
 else msg = this.vwr.getModelFileInfo ();
break;
case 1610616855:
var n = ((len = this.slen) == 2 ? 2147483647 : this.intParameter (2));
if (n < 1) this.invArg ();
if (!this.chk) {
this.vwr.sm.clearConsole ();
if (eval.scriptLevel == 0) this.vwr.removeCommand ();
msg = this.vwr.getSetHistory (n);
}break;
case 135180:
if (!this.chk) msg = this.getShapeProperty (24, "jvxlDataXml");
break;
case 1073877011:
case 1073877010:
if (eval.optParameterAsString (2).equalsIgnoreCase ("list")) {
this.e.sm.loadShape (27);
msg = (this.chk ? "" : this.getShapeProperty (27, "list -1"));
len = 3;
} else {
var ptMO = ((len = this.slen) == 2 ? -2147483648 : this.intParameter (2));
if (!this.chk) msg = this.getMoJvxl (ptMO, tok == 1073877011);
}break;
case 1094717454:
if (!this.chk) msg = this.vwr.ms.getModelInfoAsString ();
break;
case 537006096:
if (!this.chk) msg = this.vwr.getMeasurementInfoAsString ();
break;
case 1073741864:
len = 3;
if (!this.chk && this.slen == len) {
msg = this.paramAsStr (2);
msg = this.vwr.getOrientationText (JS.T.getTokFromName (msg.equals ("box") ? "volume" : msg.equals ("rotation") ? "best" : msg), "best", null).toString ();
}break;
case 1073742132:
tok = this.tokAt (2);
if (tok == 0) tok = 1073742132;
 else len = 3;
case 1073742178:
case 4129:
if (!this.chk) msg = this.vwr.getOrientationText (tok, null, null).toString ();
break;
case 1073742077:
len = 2;
if (this.slen > 3) break;
switch (tok = this.tokAt (2)) {
case 1073742178:
case 1073742132:
case 4129:
case 0:
if (!this.chk) msg = this.vwr.getOrientationText (tok, null, null).toString ();
break;
default:
name = eval.optParameterAsString (2);
msg = this.vwr.getOrientationText (1073742034, name, null).toString ();
}
len = this.slen;
break;
case 1073742088:
if (!this.chk) msg = this.vwr.ms.getPDBHeader (this.vwr.am.cmi);
break;
case 134217762:
var typ = eval.optParameterAsString (2);
if (typ.length == 0) typ = null;
len = this.slen;
if (!this.chk) msg = this.vwr.ms.getPointGroupAsString (this.vwr.bsA (), "show:" + typ, 0, 0, null, null, null);
break;
case 1088421903:
if (!this.chk) msg = this.vwr.ms.getSymmetryInfoAsString ();
break;
case 1073742176:
if (!this.chk) msg = "transform:\n" + this.vwr.tm.matrixRotate.toString ();
break;
case 4168:
msg = "zoom " + (this.vwr.tm.zoomEnabled ? ("" + this.vwr.tm.getZoomSetting ()) : "off");
break;
case 1611272202:
msg = (this.vwr.getShowFrank () ? "frank ON" : "frank OFF");
break;
case 1665140738:
str = "solventProbeRadius";
break;
case 1086324744:
if ((len = this.slen) == 3 && this.tokAt (2) == 1073742334) tok = 1086324743;
case 1073741863:
case 1086326788:
case 1073742120:
case 1113589787:
case 1086324742:
case 1140850689:
case 1073741982:
if (!this.chk) msg = this.vwr.getChimeInfo (tok);
break;
case 537022465:
case 1610612738:
case 20482:
case 1612709912:
value = "?";
break;
case 1073742030:
var qualifiers = ((len = this.slen) == 2 ? null : this.paramAsStr (2));
if (!this.chk) msg = this.vwr.getBindingInfo (qualifiers);
break;
case 1073742015:
if (!this.chk) value = this.vwr.getMenu ("");
break;
case 1073741824:
if (str.equalsIgnoreCase ("fileHeader")) {
if (!this.chk) msg = this.vwr.ms.getPDBHeader (this.vwr.am.cmi);
}break;
case 1073741992:
case 36868:
str = this.paramAsStr (len++);
var v = eval.getParameter (str, 1073742190, true);
if (!this.chk) if (tok == 1073741992) {
msg = v.toJSON ();
} else {
msg = v.escape ();
}break;
}
this.checkLength (len + filterLen);
if (this.chk) return;
if (msg != null) this.showString (this.filterShow (msg, filter));
 else if (value != null) this.showString (str + " = " + value);
 else if (str != null) {
if (str.indexOf (" ") >= 0) this.showString (str);
 else this.showString (str + " = " + (eval.getParameter (str, 1073742190, true)).escape ());
}});
Clazz.defineMethod (c$, "filterShow", 
 function (msg, name) {
if (name == null) return msg;
name = name.substring (1).toLowerCase ();
var info = JU.PT.split (msg, "\n");
var sb =  new JU.SB ();
for (var i = 0; i < info.length; i++) if (info[i].toLowerCase ().indexOf (name) >= 0) sb.append (info[i]).appendC ('\n');

return sb.toString ();
}, "~S,~S");
Clazz.defineMethod (c$, "stereo", 
 function () {
var stereoMode = J.c.STER.DOUBLE;
var degrees = -5;
var degreesSeen = false;
var colors = null;
var colorpt = 0;
for (var i = 1; i < this.slen; ++i) {
if (this.e.isColorParam (i)) {
if (colorpt > 1) this.e.bad ();
if (colorpt == 0) colors =  Clazz.newIntArray (2, 0);
if (!degreesSeen) degrees = 3;
colors[colorpt] = this.e.getArgbParam (i);
if (colorpt++ == 0) colors[1] = ~colors[0];
i = this.e.iToken;
continue;
}switch (this.getToken (i).tok) {
case 1073742335:
this.e.checkLast (this.e.iToken = 1);
this.e.iToken = 1;
break;
case 1073742334:
this.e.checkLast (this.e.iToken = 1);
stereoMode = J.c.STER.NONE;
break;
case 2:
case 3:
degrees = this.floatParameter (i);
degreesSeen = true;
break;
case 1073741824:
if (!degreesSeen) degrees = 3;
stereoMode = J.c.STER.getStereoMode (this.paramAsStr (i));
if (stereoMode != null) break;
default:
this.invArg ();
}
}
if (this.chk) return;
this.vwr.setStereoMode (colors, stereoMode, degrees);
});
Clazz.defineMethod (c$, "struts", 
 function () {
var eval = this.e;
var defOn = (this.tokAt (1) == 1073742072 || this.tokAt (1) == 1073742335 || this.slen == 1);
var mad = eval.getMadParameter ();
if (mad == 2147483647) return false;
if (defOn) mad = Math.round (this.vwr.getFloat (570425406) * 2000);
this.setShapeProperty (1, "type", Integer.$valueOf (32768));
eval.setShapeSizeBs (1, mad, null);
this.setShapeProperty (1, "type", Integer.$valueOf (1023));
return true;
});
Clazz.defineMethod (c$, "unitcell", 
 function (i) {
var eval = this.e;
var icell = 2147483647;
var mad10 = 2147483647;
var pt = null;
var tickInfo = eval.tickParamAsStr (i, true, false, false);
i = eval.iToken;
var id = null;
var oabc = null;
var newUC = null;
var ucname = null;
var isOffset = false;
var isReset = false;
var tok = this.tokAt (++i);
switch (tok) {
case 4142:
case 4141:
isReset = true;
pt = JU.P4.new4 (0, 0, 0, -1);
eval.iToken++;
break;
case 4:
case 1073741824:
var s = this.paramAsStr (i).toLowerCase ();
ucname = s;
if (s.indexOf (",") >= 0 || this.chk) {
newUC = s;
break;
}var stype = null;
eval.setCurrentCagePts (null, null);
newUC = this.vwr.getModelInfo ("unitcell_conventional");
if (JU.PT.isOneOf (ucname, ";parent;standard;primitive;")) {
if (newUC == null && this.vwr.getModelInfo ("isprimitive") != null) {
this.showString ("Cannot convert unit cell when file data is primitive and have no lattice information");
return;
}if (ucname.equals ("primitive") && this.tokAt (i + 1) == 4) stype = this.paramAsStr (++i).toUpperCase ();
}if (Clazz.instanceOf (newUC, Array)) {
oabc = newUC;
}if (stype == null) stype = this.vwr.getModelInfo ("latticeType");
if (newUC != null) eval.setCurrentCagePts (this.vwr.getV0abc (newUC), "" + newUC);
if (!ucname.equals ("conventional")) {
s = this.vwr.getModelInfo ("unitcell_" + ucname);
if (s == null) {
var isPrimitive = ucname.equals ("primitive");
if (isPrimitive || ucname.equals ("reciprocal")) {
var scale = (this.slen == i + 1 ? 1 : this.tokAt (i + 1) == 2 ? this.intParameter (++i) * 3.141592653589793 : this.floatParameter (++i));
var u = this.vwr.getCurrentUnitCell ();
ucname = (u == null ? "" : u.getSpaceGroupName () + " ") + ucname;
oabc = (u == null ?  Clazz.newArray (-1, [JU.P3.new3 (0, 0, 0), JU.P3.new3 (1, 0, 0), JU.P3.new3 (0, 1, 0), JU.P3.new3 (0, 0, 1)]) : u.getUnitCellVectors ());
if (stype == null) stype = this.vwr.getSymTemp ().getSymmetryInfoAtom (this.vwr.ms, this.vwr.getFrameAtoms ().nextSetBit (0), null, 0, null, null, null, 1073741994, 0, -1);
if (u == null) u = this.vwr.getSymTemp ();
u.toFromPrimitive (true, stype.length == 0 ? 'P' : stype.charAt (0), oabc, this.vwr.getCurrentModelAuxInfo ().get ("primitiveToCrystal"));
if (!isPrimitive) {
JU.SimpleUnitCell.getReciprocal (oabc, oabc, scale);
}break;
}} else {
ucname = s;
if (s.indexOf (",") >= 0) newUC = s;
}this.showString (ucname);
}break;
case 135180:
case 1073742330:
id = eval.objectNameParameter (++i);
break;
case 1678381065:
var o = JU.P3.newP (this.vwr.getBoundBoxCenter ());
pt = this.vwr.getBoundBoxCornerVector ();
o.sub (pt);
oabc =  Clazz.newArray (-1, [o, JU.P3.new3 (pt.x * 2, 0, 0), JU.P3.new3 (0, pt.y * 2, 0), JU.P3.new3 (0, 0, pt.z * 2)]);
pt = null;
eval.iToken = i;
break;
case 1073742176:
if (this.tokAt (++i) != 12) this.invArg ();
newUC =  Clazz.newArray (-1, [this.getToken (i).value]);
break;
case 11:
case 12:
newUC = this.getToken (i).value;
break;
case 12289:
switch (this.tokAt (++i)) {
case 12290:
case 10:
case 1073742325:
pt = this.vwr.ms.getAtomSetCenter (this.atomExpressionAt (i));
this.vwr.toFractional (pt, true);
i = eval.iToken;
break;
default:
if (eval.isCenterParameter (i)) {
pt = this.centerParameter (i);
i = eval.iToken;
break;
}this.invArg ();
}
pt.x -= 0.5;
pt.y -= 0.5;
pt.z -= 0.5;
break;
case 12290:
case 10:
case 1073742325:
var iAtom = this.atomExpressionAt (i).nextSetBit (0);
if (!this.chk) this.vwr.am.cai = iAtom;
if (iAtom < 0) return;
i = eval.iToken;
break;
case 1073742066:
isOffset = true;
case 1073742114:
pt = eval.getPointOrPlane (++i, false, true, false, true, 3, 3, true);
pt = JU.P4.new4 (pt.x, pt.y, pt.z, (isOffset ? 1 : 0));
i = eval.iToken;
break;
case 3:
case 2:
var f = this.floatParameter (i);
if (f < 111) {
i--;
break;
}icell = this.intParameter (i);
break;
default:
if (eval.isArrayParameter (i)) {
oabc = eval.getPointArray (i, 4, false);
i = eval.iToken;
} else if (this.slen > i + 1) {
pt = eval.getPointOrPlane (i, false, true, false, true, 3, 3, true);
i = eval.iToken;
} else {
i--;
}}
mad10 = eval.getSetAxesTypeMad10 (++i);
eval.checkLast (eval.iToken);
if (this.chk || mad10 == 2147483647) return;
if (mad10 == 2147483647) this.vwr.am.cai = -1;
if (oabc == null && newUC != null) oabc = this.vwr.getV0abc (newUC);
if (icell != 2147483647) this.vwr.ms.setUnitCellOffset (this.vwr.getCurrentUnitCell (), null, icell);
 else if (id != null) this.vwr.setCurrentCage (id);
 else if (isReset || oabc != null) eval.setCurrentCagePts (oabc, ucname);
eval.setObjectMad10 (33, "unitCell", mad10);
if (pt != null) this.vwr.ms.setUnitCellOffset (this.vwr.getCurrentUnitCell (), pt, 0);
if (tickInfo != null) this.setShapeProperty (33, "tickInfo", tickInfo);
}, "~N");
Clazz.defineMethod (c$, "assign", 
 function () {
var atomsOrBonds = this.tokAt (1);
var index = -1;
var index2 = -1;
if (atomsOrBonds == 1140850689 && this.tokAt (2) == 4) {
this.e.iToken++;
} else {
index = this.atomExpressionAt (2).nextSetBit (0);
if (index < 0) {
return;
}}var type = null;
if (atomsOrBonds == 4106) {
index2 = this.atomExpressionAt (++this.e.iToken).nextSetBit (0);
} else {
type = this.paramAsStr (++this.e.iToken);
}var pt = (++this.e.iToken < this.slen ? this.centerParameter (this.e.iToken) : null);
if (this.chk) return;
this.vwr.pushState ();
switch (atomsOrBonds) {
case 1140850689:
this.e.clearDefinedVariableAtomSets ();
this.assignAtom (index, pt, type);
break;
case 1677721602:
this.assignBond (index, (type + "p").charAt (0));
break;
case 4106:
this.assignConnect (index, index2);
}
});
Clazz.defineMethod (c$, "assignAtom", 
 function (atomIndex, pt, type) {
if (type.equals ("X")) this.vwr.setRotateBondIndex (-1);
if (atomIndex >= 0 && this.vwr.ms.at[atomIndex].mi != this.vwr.ms.mc - 1) return;
this.vwr.clearModelDependentObjects ();
var ac = this.vwr.ms.ac;
if (pt == null) {
if (atomIndex < 0) return;
this.vwr.sm.modifySend (atomIndex, this.vwr.ms.at[atomIndex].mi, 1, this.e.fullCommand);
this.vwr.ms.assignAtom (atomIndex, type, true, true);
if (!JU.PT.isOneOf (type, ";Mi;Pl;X;")) this.vwr.ms.setAtomNamesAndNumbers (atomIndex, -ac, null);
this.vwr.sm.modifySend (atomIndex, this.vwr.ms.at[atomIndex].mi, -1, "OK");
this.vwr.refresh (3, "assignAtom");
return;
}var atom = (atomIndex < 0 ? null : this.vwr.ms.at[atomIndex]);
var bs = (atomIndex < 0 ?  new JU.BS () : JU.BSUtil.newAndSetBit (atomIndex));
var pts =  Clazz.newArray (-1, [pt]);
var vConnections =  new JU.Lst ();
var modelIndex = -1;
if (atom != null) {
vConnections.addLast (atom);
modelIndex = atom.mi;
this.vwr.sm.modifySend (atomIndex, modelIndex, 3, this.e.fullCommand);
}try {
bs = this.vwr.addHydrogensInline (bs, vConnections, pts);
var atomIndex2 = bs.nextSetBit (0);
this.vwr.ms.assignAtom (atomIndex2, type, false, (atomIndex >= 0));
atomIndex = atomIndex2;
} catch (ex) {
if (Clazz.exceptionOf (ex, Exception)) {
} else {
throw ex;
}
}
this.vwr.ms.setAtomNamesAndNumbers (atomIndex, -ac, null);
this.vwr.sm.modifySend (atomIndex, modelIndex, -3, "OK");
}, "~N,JU.P3,~S");
Clazz.defineMethod (c$, "assignBond", 
 function (bondIndex, type) {
var modelIndex = -1;
try {
modelIndex = this.vwr.ms.bo[bondIndex].atom1.mi;
this.vwr.sm.modifySend (bondIndex, modelIndex, 2, this.e.fullCommand);
var bsAtoms = this.vwr.ms.assignBond (bondIndex, type);
if (bsAtoms == null || type == '0') this.vwr.refresh (3, "setBondOrder");
 else this.vwr.addHydrogens (bsAtoms, false, true);
this.vwr.sm.modifySend (bondIndex, modelIndex, -2, "" + type);
} catch (ex) {
if (Clazz.exceptionOf (ex, Exception)) {
JU.Logger.error ("assignBond failed");
this.vwr.sm.modifySend (bondIndex, modelIndex, -2, "ERROR " + ex);
} else {
throw ex;
}
}
}, "~N,~S");
Clazz.defineMethod (c$, "assignConnect", 
 function (index, index2) {
this.vwr.clearModelDependentObjects ();
var connections = JU.AU.newFloat2 (1);
connections[0] =  Clazz.newFloatArray (-1, [index, index2]);
var modelIndex = this.vwr.ms.at[index].mi;
this.vwr.sm.modifySend (index, modelIndex, 2, this.e.fullCommand);
this.vwr.ms.connect (connections);
this.vwr.ms.assignAtom (index, ".", true, true);
this.vwr.ms.assignAtom (index2, ".", true, true);
this.vwr.sm.modifySend (index, modelIndex, -2, "OK");
this.vwr.refresh (3, "assignConnect");
}, "~N,~N");
Clazz.defineMethod (c$, "getContext", 
 function (withVariables) {
var sb =  new JU.SB ();
var context = this.e.thisContext;
while (context != null) {
if (withVariables) {
if (context.vars != null) {
sb.append (this.getScriptID (context));
sb.append (JV.StateManager.getVariableList (context.vars, 80, true, false));
}} else {
sb.append (JS.ScriptError.getErrorLineMessage (context.functionName, context.scriptFileName, this.e.getLinenumber (context), context.pc, JS.ScriptEval.statementAsString (this.vwr, context.statement, -9999, this.e.debugHigh)));
}context = context.parentContext;
}
if (withVariables) {
if (this.e.contextVariables != null) {
sb.append (this.getScriptID (null));
sb.append (JV.StateManager.getVariableList (this.e.contextVariables, 80, true, false));
}} else {
sb.append (this.e.getErrorLineMessage2 ());
}return sb.toString ();
}, "~B");
Clazz.defineMethod (c$, "getIsosurfaceJvxl", 
 function (iShape, type) {
type = (type === "PMESH" || type === "MESH" ? "jvxlMeshX" : type === "ISOMESH" ? "pmesh" : type === "ISOMESHBIN" || type === "PMB" ? "pmeshbin" : "jvxlDataXml");
return (this.chk ? "" : this.getShapeProperty (iShape, type));
}, "~N,~S");
Clazz.defineMethod (c$, "getMoJvxl", 
 function (ptMO, isNBO) {
var iShape = (isNBO ? 28 : 27);
this.e.sm.loadShape (iShape);
var modelIndex = this.vwr.am.cmi;
if (modelIndex < 0) this.e.errorStr (30, "show/write MO/NBO");
var moData = this.vwr.ms.getInfo (modelIndex, "moData");
if (moData == null) this.error (27);
var n = this.getShapeProperty (iShape, "moNumber");
if (n == null || n.intValue () == 0) this.setShapeProperty (iShape, "init", Integer.$valueOf (modelIndex));
this.setShapeProperty (iShape, "moData", moData);
return this.e.sm.getShapePropertyIndex (iShape, "showMO", ptMO);
}, "~N,~B");
Clazz.defineMethod (c$, "getScriptID", 
 function (context) {
var fuName = (context == null ? this.e.functionName : "function " + context.functionName);
var fiName = (context == null ? this.e.scriptFileName : context.scriptFileName);
return "\n# " + fuName + " (file " + fiName + (context == null ? "" : " context " + context.id) + ")\n";
}, "JS.ScriptContext");
Clazz.defineMethod (c$, "tokenAt", 
 function (i, args) {
return (i < args.length ? args[i] : null);
}, "~N,~A");
c$.tokAtArray = Clazz.defineMethod (c$, "tokAtArray", 
 function (i, args) {
return (i < args.length && args[i] != null ? args[i].tok : 0);
}, "~N,~A");
Clazz.defineMethod (c$, "getPlotMinMax", 
 function (data, isMax, tok) {
if (data == null) return 0;
switch (tok) {
case 1111490568:
case 1111490569:
case 1111490570:
return (isMax ? 180 : -180);
case 1111490565:
case 1111490576:
return (isMax ? 360 : 0);
case 1111490574:
return (isMax ? 1 : -1);
}
var fmax = (isMax ? -1.0E10 : 1E10);
for (var i = data.length; --i >= 0; ) {
var f = data[i];
if (Float.isNaN (f)) continue;
if (isMax == (f > fmax)) fmax = f;
}
return fmax;
}, "~A,~B,~N");
Clazz.defineMethod (c$, "parseDataArray", 
 function (str, is3D) {
str = JU.Parser.fixDataString (str);
var lines = JU.Parser.markLines (str, '\n');
var nLines = lines.length;
if (!is3D) {
var data = JU.AU.newFloat2 (nLines);
for (var iLine = 0, pt = 0; iLine < nLines; pt = lines[iLine++]) {
var tokens = JU.PT.getTokens (str.substring (pt, lines[iLine]));
JU.PT.parseFloatArrayData (tokens, data[iLine] =  Clazz.newFloatArray (tokens.length, 0));
}
return data;
}var tokens = JU.PT.getTokens (str.substring (0, lines[0]));
if (tokens.length != 3) return  Clazz.newFloatArray (0, 0, 0, 0);
var nX = JU.PT.parseInt (tokens[0]);
var nY = JU.PT.parseInt (tokens[1]);
var nZ = JU.PT.parseInt (tokens[2]);
if (nX < 1 || nY < 1 || nZ < 1) return  Clazz.newFloatArray (1, 1, 1, 0);
var data = JU.AU.newFloat3 (nX, nY);
var iX = 0;
var iY = 0;
for (var iLine = 1, pt = lines[0]; iLine < nLines && iX < nX; pt = lines[iLine++]) {
tokens = JU.PT.getTokens (str.substring (pt, lines[iLine]));
if (tokens.length < nZ) continue;
JU.PT.parseFloatArrayData (tokens, data[iX][iY] =  Clazz.newFloatArray (tokens.length, 0));
if (++iY == nY) {
iX++;
iY = 0;
}}
if (iX != nX) {
System.out.println ("Error reading 3D data -- nX = " + nX + ", but only " + iX + " blocks read");
return  Clazz.newFloatArray (1, 1, 1, 0);
}return data;
}, "~S,~B");
Clazz.defineMethod (c$, "getBitsetPropertyFloat", 
function (bs, tok, property, min, max) {
var odata = (property == null || tok == (1111490843) ? this.e.getBitsetProperty (bs, null, tok, null, null, property, null, false, 2147483647, false) : this.vwr.getDataObj (property, bs, 1));
if (odata == null || !JU.AU.isAF (odata)) return (bs == null ? null :  Clazz.newFloatArray (bs.cardinality (), 0));
var data = odata;
if (!Float.isNaN (min)) for (var i = 0; i < data.length; i++) if (data[i] < min) data[i] = NaN;

if (!Float.isNaN (max)) for (var i = 0; i < data.length; i++) if (data[i] > max) data[i] = NaN;

return data;
}, "JU.BS,~N,~S,~N,~N");
Clazz.defineStatics (c$,
"ERROR_invalidArgument", 22);
});